Variant report

Variant	rs1999979
Chromosome Location	chr9:2018658-2018659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr9:2017492-2019116	Hela-S3	cervix:	n/a	chr9:2018337-2018350 chr9:2018337-2018348
2	MYC	chr9:2016009-2019058	K562	blood:	n/a	chr9:2017021-2017031 chr9:2017316-2017326 chr9:2016478-2016487
3	POLR2A	chr9:2017178-2018699	GM12892	blood:	n/a	n/a
4	FOS	chr9:2018567-2018726	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT5A	chr9:2018634-2019421	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:2013421-2019552	GM12878	blood:	n/a	n/a
7	CHD1	chr9:2014303-2019408	GM12878	blood:	n/a	chr9:2016689-2016699 chr9:2015110-2015120
8	POLR2A	chr9:2014174-2019412	GM12892	blood:	n/a	n/a
9	POLR2A	chr9:2013483-2019507	GM12891	blood:	n/a	n/a
10	POLR2A	chr9:2014061-2019440	GM12878	blood:	n/a	n/a
11	MYC	chr9:2014702-2018960	NB4	blood:	n/a	chr9:2017021-2017031 chr9:2015855-2015865 chr9:2017316-2017326 chr9:2015105-2015115 chr9:2016478-2016487
12	POU5F1	chr9:2018643-2019180	H1-hESC	embryonic stem cell:	n/a	chr9:2019051-2019065 chr9:2018957-2018971 chr9:2018957-2018971 chr9:2018958-2018972 chr9:2018799-2018813 chr9:2018798-2018812 chr9:2018957-2018971 chr9:2019051-2019065 chr9:2018798-2018812 chr9:2018798-2018812
13	WRNIP1	chr9:2017355-2019393	GM12878	blood:	n/a	n/a
14	CEBPB	chr9:2018131-2018670	K562	blood:	n/a	chr9:2018337-2018350 chr9:2018337-2018348
15	RFX5	chr9:2018132-2018896	K562	blood:	n/a	n/a
16	POLR2A	chr9:2014031-2019520	GM12878	blood:	n/a	n/a
17	POLR2A	chr9:2015971-2018999	PBDE	blood:	n/a	n/a
18	MXI1	chr9:2013524-2018820	IMR90	lung:	n/a	n/a
19	MXI1	chr9:2013880-2018757	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr9:2014520-2018704	GM12892	blood:	n/a	n/a
21	POLR2A	chr9:2013926-2018823	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:2014683..2019202-chr9:2026620..2030174,6	MCF-7	breast:
2	chr9:2013479..2017608-chr9:2017826..2022083,7	MCF-7	breast:
3	chr9:2016568..2019114-chr9:2030660..2033552,2	MCF-7	breast:
4	chr9:2018308..2020609-chr9:2085608..2087272,2	K562	blood:

Variant related genes	Relation type
SMARCA2	TF binding region
ENSG00000080503	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10757122	0.90[LWK][hapmap]
rs10964466	0.90[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1021712	chr9:1647840-2216839	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv539921	chr9:1647840-2216839	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS 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 target site	14 gene(s)	inside rSNPs	diseases
5	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv831493	chr9:1885733-2074135	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv892047	chr9:1888703-2018825	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv892048	chr9:1888703-2177391	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1021158	chr9:1963930-2040728	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv892052	chr9:1980819-2072470	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv2830420	chr9:1998911-2119702	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv613079	chr9:2012767-2059341	Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2013800-2018800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:2014000-2018800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:2014000-2019200	Active TSS	Aorta	Aorta
4	chr9:2014000-2019200	Active TSS	Ovary	ovary
5	chr9:2014000-2019600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr9:2014000-2020000	Active TSS	Right Atrium	heart
7	chr9:2014200-2018800	Active TSS	Brain Hippocampus Middle	brain
8	chr9:2014200-2018800	Active TSS	Brain Substantia Nigra	brain
9	chr9:2014200-2018800	Active TSS	Left Ventricle	heart
10	chr9:2014200-2018800	Active TSS	Psoas Muscle	Psoas
11	chr9:2014200-2018800	Active TSS	HSMMtube	muscle
12	chr9:2014200-2019200	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr9:2014200-2021400	Active TSS	GM12878-XiMat	blood
14	chr9:2014400-2018800	Active TSS	Fetal Stomach	stomach
15	chr9:2014400-2018800	Active TSS	K562	blood
16	chr9:2014400-2019400	Active TSS	Fetal Muscle Trunk	muscle
17	chr9:2014600-2019000	Active TSS	Lung	lung
18	chr9:2014600-2019400	Active TSS	Placenta	Placenta
19	chr9:2014800-2018800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:2015000-2018800	Active TSS	Colonic Mucosa	Colon
21	chr9:2016000-2019200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr9:2016400-2018800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:2016400-2018800	Active TSS	Primary T cells fromperipheralblood	blood
24	chr9:2016400-2019000	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr9:2016800-2018800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:2017800-2018800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:2017800-2019200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
28	chr9:2017800-2019600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr9:2017800-2019800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr9:2018000-2018800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr9:2018000-2019000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
32	chr9:2018000-2019200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr9:2018000-2019200	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr9:2018000-2019600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
35	chr9:2018000-2019600	Flanking Active TSS	Fetal Brain Male	brain
36	chr9:2018000-2020800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr9:2018000-2028200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:2018200-2018800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
39	chr9:2018200-2018800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:2018200-2018800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr9:2018200-2019000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr9:2018200-2019000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
43	chr9:2018200-2019000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr9:2018200-2019000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
45	chr9:2018200-2019000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr9:2018200-2019000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr9:2018200-2019000	Flanking Active TSS	HSMM	muscle
48	chr9:2018200-2019000	Flanking Active TSS	HUVEC	blood vessel
49	chr9:2018200-2019000	Flanking Active TSS	Osteobl	bone
50	chr9:2018200-2019200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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