Variant report

Variant	rs3750384
Chromosome Location	chr9:140449722-140449723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:140449488-140450360	GM12892	blood:	n/a	n/a
2	POLR2A	chr9:140449495-140450378	K562	blood:	n/a	n/a
3	POLR2A	chr9:140448951-140449844	K562	blood:	n/a	n/a
4	POLR2A	chr9:140449587-140449735	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr9:140449719-140449839	MCF-7	breast:	n/a	n/a
6	POLR2A	chr9:140449580-140450012	GM12892	blood:	n/a	n/a
7	POLR2A	chr9:140446225-140450742	K562	blood:	n/a	n/a
8	GTF2F1	chr9:140449705-140449813	K562	blood:	n/a	n/a
9	POLR2A	chr9:140449424-140450081	HepG2	liver:	n/a	n/a
10	POLR2A	chr9:140449673-140449966	GM12878	blood:	n/a	n/a
11	POLR2A	chr9:140449544-140449729	HepG2	liver:	n/a	n/a
12	POLR2A	chr9:140449361-140450377	K562	blood:	n/a	n/a
13	POLR2A	chr9:140449494-140449991	HL-60	blood:	n/a	n/a
14	POLR2A	chr9:140449590-140450093	GM12891	blood:	n/a	n/a
15	POLR2A	chr9:140449703-140449836	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr9:140449419-140449904	K562	blood:	n/a	n/a
17	POLR2A	chr9:140449367-140450311	GM12878	blood:	n/a	n/a
18	POLR2A	chr9:140449508-140449967	GM12878	blood:	n/a	n/a
19	POLR2A	chr9:140449408-140449902	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr9:140449681-140449960	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr9:140449409-140449927	GM12891	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:140445810..140448101-chr9:140449501..140452314,4	K562	blood:
2	chr9:140447442..140450048-chr9:140483763..140485400,2	MCF-7	breast:
3	chr9:140443477..140447796-chr9:140449022..140451330,7	MCF-7	breast:
4	chr9:140449572..140452200-chr9:140506963..140508845,2	MCF-7	breast:
5	chr9:140193137..140197903-chr9:140443164..140449787,14	MCF-7	breast:
6	chr9:140448023..140449747-chr9:140465385..140467974,2	K562	blood:
7	chr9:140448822..140451446-chr9:140457626..140459240,2	K562	blood:
8	chr9:140447426..140450339-chr9:140645965..140648548,2	K562	blood:

No data

Variant related genes	Relation type
PNPLA7	TF binding region
ENSG00000198435	Chromatin interaction
ENSG00000197070	Chromatin interaction
ENSG00000182154	Chromatin interaction
ENSG00000130653	Chromatin interaction
ENSG00000165724	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11507687	1.00[CHD][hapmap]
rs11522284	1.00[CHD][hapmap]
rs11541259	1.00[CHD][hapmap]
rs11559482	1.00[MEX][hapmap]
rs12156648	1.00[CHD][hapmap]
rs12236403	1.00[CHD][hapmap]
rs13284456	1.00[CHD][hapmap]
rs17855638	1.00[MEX][hapmap]
rs2298171	1.00[CHD][hapmap]
rs28563072	1.00[CHD][hapmap]
rs28657895	1.00[CHD][hapmap]
rs28859278	1.00[CHD][hapmap]
rs7029134	1.00[CHD][hapmap]
rs7034073	1.00[MEX][hapmap]
rs821314	1.00[CHD][hapmap]
rs872341	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894442	chr9:139544437-140462099	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv894523	chr9:139860631-140462099	Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	nsv894663	chr9:140382705-140454791	Weak transcription Strong transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
26	nsv540362	chr9:140401645-140452700	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	n/a
27	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
28	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
29	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
30	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
31	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
32	nsv894664	chr9:140442503-140454791	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	n/a
33	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140446800-140459800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:140447000-140450400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:140447000-140464200	Weak transcription	Fetal Kidney	kidney
4	chr9:140447200-140449800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:140447200-140449800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr9:140447200-140449800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr9:140447200-140450800	Weak transcription	Fetal Lung	lung
8	chr9:140447200-140452600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr9:140447200-140458200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr9:140447200-140458200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr9:140447200-140459400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr9:140447200-140466400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:140447200-140470200	Weak transcription	Stomach Mucosa	stomach
14	chr9:140447200-140471800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:140447400-140449800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:140447400-140449800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr9:140447400-140450200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:140447400-140450200	Weak transcription	HSMM	muscle
19	chr9:140447400-140450200	Weak transcription	HUVEC	blood vessel
20	chr9:140447400-140450400	Weak transcription	Fetal Heart	heart
21	chr9:140447400-140450400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr9:140447400-140450600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:140447400-140450600	Strong transcription	Fetal Intestine Small	intestine
24	chr9:140447400-140450800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:140447400-140451200	Weak transcription	Fetal Brain Male	brain
26	chr9:140447400-140452000	Strong transcription	A549	lung
27	chr9:140447400-140452600	Weak transcription	NH-A	brain
28	chr9:140447400-140453400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:140447400-140453400	Strong transcription	Thymus	Thymus
30	chr9:140447400-140459800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:140447400-140466400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr9:140447400-140466800	Weak transcription	Psoas Muscle	Psoas
33	chr9:140447400-140469400	Weak transcription	Right Atrium	heart
34	chr9:140447400-140471800	Weak transcription	Small Intestine	intestine
35	chr9:140447600-140449800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:140447600-140455000	Strong transcription	Spleen	Spleen
37	chr9:140447600-140458800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:140447600-140459600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:140447600-140459800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:140447600-140459800	Strong transcription	Fetal Stomach	stomach
41	chr9:140447800-140450400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr9:140447800-140453400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:140447800-140455000	Strong transcription	Lung	lung
44	chr9:140448000-140459600	Strong transcription	Fetal Brain Female	brain
45	chr9:140448400-140450000	Strong transcription	Fetal Thymus	thymus
46	chr9:140448400-140459600	Strong transcription	Fetal Intestine Large	intestine
47	chr9:140448800-140459800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:140449000-140450200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:140449000-140450200	Strong transcription	Fetal Muscle Leg	muscle
50	chr9:140449000-140451000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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