Variant report

Variant	rs1397195
Chromosome Location	chr3:156388495-156388496
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156384119..156388903-chr3:156389462..156394403,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11710516	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1355280	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1397194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1510270	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs168245	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs168295	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs171077	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs180746	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs180747	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs182935	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs182936	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs184677	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858229	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs186928	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193423	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054881	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129909	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136691	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2136692	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs237245	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs237246	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2665390	0.84[ASN][1000 genomes]
rs343991	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343995	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343996	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343997	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343998	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344000	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344001	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344006	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344008	0.84[ASN][1000 genomes]
rs344009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344015	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344016	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs344017	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344023	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344029	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs344032	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344047	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344048	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344049	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344050	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs344052	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344053	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344054	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344055	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344058	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344059	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344060	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344061	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs344062	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344063	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs344064	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344065	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344066	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344068	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344069	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344070	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs345987	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs419287	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427384	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4279048	0.94[ASN][1000 genomes]
rs4429586	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4679784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680297	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680298	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680299	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5012666	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441089	0.83[AMR][1000 genomes]
rs6441092	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441093	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441094	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6441095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6799457	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7640593	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs871232	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs871233	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs907063	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs931990	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs978108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs978109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823112	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833951	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9877043	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 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	chr3:156382600-156391600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:156383000-156391400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:156383600-156390600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:156384200-156391400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:156384200-156391400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:156385600-156390600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:156386200-156391600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:156386400-156390800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:156386400-156391200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:156386400-156391200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:156386400-156391200	Weak transcription	NHEK	skin
12	chr3:156386400-156391400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:156386400-156391400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:156386400-156391400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:156386400-156391400	Weak transcription	Fetal Intestine Small	intestine
16	chr3:156386400-156391600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr3:156386400-156391600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:156386400-156391600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:156386600-156388600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:156386600-156389200	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr3:156386600-156390600	Weak transcription	HepG2	liver
22	chr3:156386600-156391200	Weak transcription	Liver	Liver
23	chr3:156386600-156391400	Weak transcription	Primary T cells from cord blood	blood
24	chr3:156386600-156391400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:156386600-156391400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:156386600-156391400	Weak transcription	A549	lung
27	chr3:156386600-156391400	Weak transcription	HMEC	breast
28	chr3:156386600-156391600	Weak transcription	Fetal Lung	lung
29	chr3:156386800-156391200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:156386800-156391200	Weak transcription	GM12878-XiMat	blood
31	chr3:156386800-156391200	Weak transcription	K562	blood
32	chr3:156386800-156391600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:156386800-156391600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:156386800-156391600	Weak transcription	Fetal Intestine Large	intestine
35	chr3:156386800-156391600	Weak transcription	NHLF	lung
36	chr3:156387000-156391000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:156387000-156391200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:156387000-156391200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:156387000-156391200	Weak transcription	Hela-S3	cervix
40	chr3:156387000-156391400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:156387000-156391400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:156387000-156391400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:156387000-156391600	Weak transcription	NHDF-Ad	bronchial
44	chr3:156387400-156391200	Weak transcription	Small Intestine	intestine
45	chr3:156387400-156391400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:156387800-156388600	Enhancers	HUVEC	blood vessel
47	chr3:156388000-156389600	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr3:156388200-156391400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:156388200-156391600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:156388200-156391600	Weak transcription	Stomach Mucosa	stomach

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