Variant report

Variant	rs3828996
Chromosome Location	chr7:33195526-33195527
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	FOS	chr7:33195487-33195686	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr7:33195444-33195793	U87	brain:	n/a	n/a
3	PBX3	chr7:33195458-33196439	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr7:33195292-33196550	SK-N-SH	brain:	n/a	n/a
5	FOS	chr7:33195450-33195723	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr7:33195445-33195753	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr7:33195417-33195731	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr7:33195511-33195721	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr7:33195416-33195800	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
BBS9	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1019301	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10269945	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10274959	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10486525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10486527	1.00[CHB][hapmap]
rs11982012	1.00[CHB][hapmap]
rs12155389	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs1362370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16879114	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17169807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17169808	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17170099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17170104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17170105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17170120	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17170131	0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17170138	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17170140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17170143	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17170155	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17170167	0.82[AMR][1000 genomes]
rs17170169	0.82[AMR][1000 genomes]
rs17170189	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs2392229	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34950347	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3750122	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4538777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4628178	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55829345	0.91[EUR][1000 genomes]
rs55847945	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55865959	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55924837	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56076132	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56195645	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58550767	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59075362	0.81[ASN][1000 genomes]
rs59446325	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60146993	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60268357	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60491621	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60871858	0.82[EUR][1000 genomes]
rs6943198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6944559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6952244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6955645	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs6964836	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6969284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6973114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6973552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73307386	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73307398	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73307399	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73307400	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73307592	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73309308	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73309310	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73309312	0.82[AMR][1000 genomes]
rs73309316	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73309318	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73309324	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73309326	0.81[ASN][1000 genomes]
rs73309328	0.81[ASN][1000 genomes]
rs73309405	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73309423	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73313121	0.82[AMR][1000 genomes]
rs73317492	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73319406	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73319407	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73319408	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73688093	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73689881	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7459365	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7781504	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7793667	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7795704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7796922	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7798118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7799346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7808472	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7809235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7809366	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9791555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9791901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029220	chr7:32921484-33262190	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv830942	chr7:33048075-33246735	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv606609	chr7:33131729-33196354	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers 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	12 gene(s)	inside rSNPs	diseases
4	nsv830943	chr7:33167106-33352759	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv933792	chr7:33169693-33216984	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:33170200-33205800	Weak transcription	Aorta	Aorta
2	chr7:33171200-33196200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:33171200-33205800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr7:33171200-33206600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:33176400-33206000	Weak transcription	Liver	Liver
6	chr7:33182400-33210200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr7:33182800-33205600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:33184600-33205800	Weak transcription	Fetal Lung	lung
9	chr7:33184800-33217200	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:33185000-33205800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:33185200-33196200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:33185400-33196400	Weak transcription	Brain Substantia Nigra	brain
13	chr7:33185400-33196800	Weak transcription	Brain Anterior Caudate	brain
14	chr7:33185400-33218000	Weak transcription	Brain Angular Gyrus	brain
15	chr7:33185600-33205600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:33185600-33224000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:33187000-33196400	Weak transcription	Adipose Nuclei	Adipose
18	chr7:33189000-33197200	Weak transcription	HSMMtube	muscle
19	chr7:33189200-33206800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr7:33190000-33217600	Weak transcription	Left Ventricle	heart
21	chr7:33190200-33230400	Weak transcription	Gastric	stomach
22	chr7:33190400-33197400	Weak transcription	Colon Smooth Muscle	Colon
23	chr7:33191400-33205800	Weak transcription	Fetal Intestine Large	intestine
24	chr7:33191600-33205800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr7:33191800-33196600	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:33191800-33199600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:33192000-33197400	Weak transcription	Fetal Heart	heart
28	chr7:33192000-33205600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr7:33192200-33195600	Weak transcription	Fetal Kidney	kidney
30	chr7:33192200-33199800	Weak transcription	Primary B cells from cord blood	blood
31	chr7:33192400-33195800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:33192600-33205000	Weak transcription	Fetal Stomach	stomach
33	chr7:33192800-33196000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:33193000-33196600	Weak transcription	Small Intestine	intestine
35	chr7:33193000-33205600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr7:33193200-33197600	Strong transcription	Primary T cells from cord blood	blood
37	chr7:33193400-33197800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:33193600-33205800	Weak transcription	Fetal Brain Female	brain
39	chr7:33194000-33205800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:33194200-33196200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:33194200-33197800	Enhancers	Osteobl	bone
42	chr7:33194400-33196600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:33194600-33198000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:33194600-33205800	Weak transcription	Ovary	ovary
45	chr7:33194600-33205800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr7:33194800-33195800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr7:33194800-33197400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:33195200-33197800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr7:33195200-33206400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr7:33195200-33220200	Weak transcription	Primary T cells fromperipheralblood	blood

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