Variant report

Variant	rs539468761
Chromosome Location	chr9:140474558-140474559
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:140474315-140477530	K562	blood:	n/a	n/a
2	POLR2A	chr9:140474497-140476592	GM12892	blood:	n/a	n/a
3	POLR2A	chr9:140474430-140475702	GM12891	blood:	n/a	n/a
4	POLR2A	chr9:140474459-140474796	K562	blood:	n/a	n/a
5	POLR2A	chr9:140474340-140476705	HL-60	blood:	n/a	n/a
6	POLR2A	chr9:140474230-140476379	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr9:140474508-140475382	GM12892	blood:	n/a	n/a
8	POLR2A	chr9:140474551-140474825	GM12878	blood:	n/a	n/a
9	POLR2A	chr9:140474558-140474589	HepG2	liver:	n/a	n/a
10	POLR2A	chr9:140474448-140477014	K562	blood:	n/a	n/a
11	POLR2A	chr9:140474535-140474811	A549	lung:	n/a	n/a
12	POLR2A	chr9:140474396-140476534	GM12878	blood:	n/a	n/a
13	POLR2A	chr9:140474303-140475311	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr9:140474445-140476668	GM12892	blood:	n/a	n/a
15	POLR2A	chr9:140474556-140475665	GM12878	blood:	n/a	n/a
16	POLR2A	chr9:140474428-140476693	K562	blood:	n/a	n/a
17	CTCF	chr9:140474540-140474690	GM12873	blood:	n/a	n/a
18	POLR2A	chr9:140474431-140475664	GM12891	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:140469278..140479132-chr9:140503165..140510984,27	MCF-7	breast:
2	chr9:140469283..140475998-chr9:140510945..140517022,12	K562	blood:
3	chr9:140470766..140479486-chr9:140497266..140502997,13	MCF-7	breast:
4	chr9:140470852..140475352-chr9:140511735..140515041,9	MCF-7	breast:
5	chr9:140473450..140475457-chr9:140537565..140540083,2	K562	blood:
6	chr9:140439204..140441132-chr9:140473629..140475589,2	MCF-7	breast:
7	chr9:140473863..140476150-chr9:140498487..140501335,2	K562	blood:
8	chr9:140444243..140447461-chr9:140473220..140477204,4	MCF-7	breast:
9	chr9:140473487..140475608-chr9:140520167..140523048,2	K562	blood:
10	chr9:140470526..140476841-chr9:140479974..140487037,14	MCF-7	breast:
11	chr9:140135182..140137272-chr9:140472466..140474673,2	K562	blood:
12	chr9:140473011..140477060-chr9:140511720..140517022,6	K562	blood:
13	chr9:140443274..140446260-chr9:140471876..140474598,3	K562	blood:
14	chr9:140473638..140477283-chr9:140490504..140494912,4	K562	blood:
15	chr9:140470445..140476327-chr9:140498022..140503450,9	K562	blood:
16	chr9:140444420..140448721-chr9:140471876..140474832,3	K562	blood:

No data

Variant related genes	Relation type
DPH7	TF binding region
ENSG00000181090	Chromatin interaction
ENSG00000182154	Chromatin interaction
ENSG00000197070	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000165724	Chromatin interaction
ENSG00000130653	Chromatin interaction
ENSG00000203993	Chromatin interaction
ENSG00000263933	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894452	chr9:139598108-140523429	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	nsv894499	chr9:139810595-140734161	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
3	nsv894502	chr9:139823670-140487108	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
4	nsv531664	chr9:140110329-140725056	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	275 gene(s)	inside rSNPs	diseases
5	nsv531654	chr9:140110329-141033187	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	281 gene(s)	inside rSNPs	diseases
6	nsv1047563	chr9:140219047-140560852	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
7	nsv540357	chr9:140219047-140560852	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
8	nsv531602	chr9:140240417-140535223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	diseases
9	nsv932633	chr9:140240417-141053535	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
10	nsv1035524	chr9:140251014-140751633	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
11	nsv1053628	chr9:140260666-141005637	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
12	nsv534215	chr9:140286134-141008915	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	n/a
13	nsv1035388	chr9:140306746-140654768	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	n/a
14	nsv831762	chr9:140338779-140514107	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	n/a
15	nsv1039672	chr9:140343466-140707505	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
16	nsv540358	chr9:140343466-140707505	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
17	nsv1041512	chr9:140350404-140612859	Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
18	nsv540359	chr9:140350404-140612859	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
19	nsv616022	chr9:140372570-140523429	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	n/a
20	nsv616023	chr9:140372570-140602887	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
21	nsv531603	chr9:140378700-140590977	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
22	nsv531665	chr9:140378700-141073897	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	n/a
23	nsv868924	chr9:140407572-141053525	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	n/a
24	nsv1039933	chr9:140408112-141005637	Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
25	nsv531666	chr9:140409395-141015925	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
26	nsv616024	chr9:140414410-140536098	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	n/a
27	nsv831763	chr9:140439831-140614021	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	n/a
28	nsv540364	chr9:140447860-140514807	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	n/a
29	esv3398333	chr9:140451462-140814795	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	n/a
30	nsv1052036	chr9:140452641-141018985	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
31	nsv540365	chr9:140452641-141018985	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
32	nsv949702	chr9:140466816-141027939	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	n/a
33	nsv531667	chr9:140468821-140936261	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
34	nsv894665	chr9:140469600-140523429	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	n/a
35	nsv894666	chr9:140470564-140518576	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	n/a
36	nsv894667	chr9:140473729-140518576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140472600-140474600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:140473400-140476200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:140473400-140480000	Weak transcription	Small Intestine	intestine
4	chr9:140473800-140474800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:140473800-140475400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:140473800-140475800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:140473800-140476000	Weak transcription	Primary T cells from cord blood	blood
8	chr9:140473800-140476400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:140473800-140483600	Weak transcription	Fetal Kidney	kidney
10	chr9:140473800-140483800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:140474000-140474600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr9:140474000-140474600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr9:140474000-140474600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:140474000-140474600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr9:140474000-140474600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:140474000-140474600	Weak transcription	Brain Angular Gyrus	brain
17	chr9:140474000-140474600	Weak transcription	Brain Anterior Caudate	brain
18	chr9:140474000-140474600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:140474000-140474600	Weak transcription	Fetal Intestine Small	intestine
20	chr9:140474000-140474600	Enhancers	Placenta	Placenta
21	chr9:140474000-140474600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr9:140474000-140474600	Weak transcription	A549	lung
23	chr9:140474000-140474800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr9:140474000-140474800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:140474000-140474800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr9:140474000-140474800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr9:140474000-140474800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr9:140474000-140474800	Enhancers	Liver	Liver
29	chr9:140474000-140474800	Weak transcription	Esophagus	oesophagus
30	chr9:140474000-140474800	Enhancers	Right Ventricle	heart
31	chr9:140474000-140475000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:140474000-140475000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:140474000-140475000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr9:140474000-140475000	Weak transcription	Fetal Brain Female	brain
35	chr9:140474000-140475000	Weak transcription	Gastric	stomach
36	chr9:140474000-140475000	Weak transcription	Thymus	Thymus
37	chr9:140474000-140475000	Enhancers	NH-A	brain
38	chr9:140474000-140475000	Weak transcription	NHEK	skin
39	chr9:140474000-140475000	Weak transcription	NHLF	lung
40	chr9:140474000-140475200	Enhancers	Adipose Nuclei	Adipose
41	chr9:140474000-140475200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:140474000-140475400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr9:140474000-140475400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:140474000-140475400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr9:140474000-140475400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr9:140474000-140475400	Weak transcription	Spleen	Spleen
47	chr9:140474000-140475600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr9:140474000-140475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:140474000-140475600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr9:140474000-140475600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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