Variant report

Variant	rs12531774
Chromosome Location	chr7:40034083-40034084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:40030873..40032517-chr7:40032744..40035272,2	MCF-7	breast:

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10156182	0.88[ASN][1000 genomes]
rs10233552	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10234693	0.90[ASN][1000 genomes]
rs10246466	0.92[ASN][1000 genomes]
rs1024680	0.90[ASN][1000 genomes]
rs10252631	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10254394	0.89[ASN][1000 genomes]
rs10261984	0.82[EUR][1000 genomes]
rs10272641	0.90[ASN][1000 genomes]
rs10275761	0.92[ASN][1000 genomes]
rs1082028	0.82[ASN][1000 genomes]
rs10951623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10951624	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10951625	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11972983	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11977756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11980745	0.93[ASN][1000 genomes]
rs11983287	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12334141	0.88[ASN][1000 genomes]
rs12530835	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12531761	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532714	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12533272	0.90[ASN][1000 genomes]
rs12534103	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12535281	0.87[EUR][1000 genomes]
rs12536190	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12536349	0.92[EUR][1000 genomes]
rs12536726	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12537125	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12537320	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12539956	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1257698	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1257699	0.83[ASN][1000 genomes]
rs12666454	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12669872	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12672040	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12672136	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12672142	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13438258	0.87[EUR][1000 genomes]
rs13438262	0.87[EUR][1000 genomes]
rs13438324	0.87[EUR][1000 genomes]
rs1403381	0.93[ASN][1000 genomes]
rs17171637	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17171645	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17171646	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17496429	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17496670	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17496733	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17537767	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17538125	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2015842	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2052097	0.90[ASN][1000 genomes]
rs2077124	0.88[ASN][1000 genomes]
rs2109339	0.91[ASN][1000 genomes]
rs2159488	0.82[ASN][1000 genomes]
rs2159489	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2302341	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2329615	0.87[EUR][1000 genomes]
rs2329693	0.88[ASN][1000 genomes]
rs28627647	0.84[EUR][1000 genomes]
rs28879668	0.87[EUR][1000 genomes]
rs33999222	0.92[ASN][1000 genomes]
rs3735135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3800799	0.98[EUR][1000 genomes]
rs3800802	0.84[ASN][1000 genomes]
rs3801238	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3847019	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3847020	0.85[ASN][1000 genomes]
rs3847021	0.81[ASN][1000 genomes]
rs3911836	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3911889	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4344004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4720344	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4720347	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4720348	0.89[ASN][1000 genomes]
rs4720349	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4723923	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4723925	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723927	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4723928	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60315659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6952597	0.82[ASN][1000 genomes]
rs6960111	0.90[ASN][1000 genomes]
rs6961040	0.87[EUR][1000 genomes]
rs6963973	0.87[EUR][1000 genomes]
rs6966917	0.89[ASN][1000 genomes]
rs6967332	0.87[EUR][1000 genomes]
rs6970469	0.84[EUR][1000 genomes]
rs6975853	0.81[ASN][1000 genomes]
rs731847	0.88[ASN][1000 genomes]
rs731848	0.88[ASN][1000 genomes]
rs73394665	0.82[ASN][1000 genomes]
rs758696	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs773385	0.83[ASN][1000 genomes]
rs773386	0.83[ASN][1000 genomes]
rs773393	0.97[ASN][1000 genomes]
rs773397	0.97[ASN][1000 genomes]
rs773402	0.92[ASN][1000 genomes]
rs773410	0.86[ASN][1000 genomes]
rs773411	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs773413	0.92[ASN][1000 genomes]
rs773414	0.82[ASN][1000 genomes]
rs773424	0.83[ASN][1000 genomes]
rs7779663	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7797041	0.90[ASN][1000 genomes]
rs7799846	0.93[ASN][1000 genomes]
rs940272	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9639818	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv1015322	chr7:40006195-40141195	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv2761319	chr7:40006195-40142139	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv464436	chr7:40018693-40133044	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv606706	chr7:40018693-40133044	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv606707	chr7:40021044-40133044	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv606708	chr7:40021044-40157040	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv887978	chr7:40030488-40124137	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39993600-40048200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:39995200-40042600	Weak transcription	K562	blood
3	chr7:40018600-40047800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:40020000-40037400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:40020400-40077600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:40023400-40046800	Weak transcription	HMEC	breast
7	chr7:40023800-40043200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr7:40025600-40035600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:40025600-40037200	Weak transcription	Fetal Lung	lung
10	chr7:40025600-40042600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr7:40025600-40046800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr7:40025600-40055400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:40025800-40035000	Weak transcription	GM12878-XiMat	blood
14	chr7:40025800-40039600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:40025800-40043200	Weak transcription	Left Ventricle	heart
16	chr7:40025800-40054800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr7:40025800-40055400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:40025800-40055400	Weak transcription	Fetal Heart	heart
19	chr7:40025800-40055400	Weak transcription	Stomach Mucosa	stomach
20	chr7:40025800-40059600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr7:40025800-40062800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr7:40025800-40082200	Weak transcription	Spleen	Spleen
23	chr7:40026000-40071200	Weak transcription	Brain Germinal Matrix	brain
24	chr7:40026400-40036800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr7:40026600-40096800	Weak transcription	Right Ventricle	heart
26	chr7:40027400-40045400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:40027600-40042000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr7:40027600-40042400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:40027600-40042400	Weak transcription	Esophagus	oesophagus
30	chr7:40027600-40043200	Weak transcription	Pancreas	Pancrea
31	chr7:40027800-40042200	Weak transcription	Osteobl	bone
32	chr7:40027800-40047400	Weak transcription	Fetal Kidney	kidney
33	chr7:40027800-40047600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr7:40027800-40047800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr7:40027800-40048400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr7:40027800-40049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:40027800-40053800	Weak transcription	HepG2	liver
38	chr7:40027800-40054800	Weak transcription	Aorta	Aorta
39	chr7:40027800-40055400	Weak transcription	Fetal Brain Female	brain
40	chr7:40028000-40037000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:40028000-40037000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr7:40028000-40037200	Weak transcription	Primary T cells from cord blood	blood
43	chr7:40028000-40038600	Weak transcription	HUVEC	blood vessel
44	chr7:40028000-40039000	Weak transcription	Liver	Liver
45	chr7:40028000-40039600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:40028000-40040200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr7:40028000-40042400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:40028000-40042400	Weak transcription	Fetal Intestine Large	intestine
49	chr7:40028000-40042800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr7:40028000-40043000	Weak transcription	NHEK	skin

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