Variant report

Variant	rs2686374
Chromosome Location	chr12:121609953-121609954
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	chr12:121609945..121611555-chr12:121644993..121647388,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11065468	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065469	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065470	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065471	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1618709	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1619628	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1621388	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1626329	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1653598	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1653601	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1653602	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1653603	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1653605	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1653610	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1653611	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1653612	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1653614	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1653616	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1653617	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1653618	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1718108	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1718119	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1718130	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1718131	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1718132	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1718133	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1718134	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1718135	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1718136	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1718137	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1718160	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2567986	0.86[AFR][1000 genomes]
rs2567988	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2567989	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2567991	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2567997	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2567999	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2568001	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2568002	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2568003	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2686373	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686375	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2686378	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2686379	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686380	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686384	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686385	0.92[ASN][1000 genomes]
rs2857591	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2857592	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915641	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35734276	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs504677	0.87[ASN][1000 genomes]
rs531095	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7137047	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs891781	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats 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 target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121571800-121623200	Weak transcription	Colonic Mucosa	Colon
2	chr12:121583000-121613200	Weak transcription	Primary B cells from cord blood	blood
3	chr12:121583000-121634600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:121583800-121623600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:121583800-121634400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:121584600-121626600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:121586200-121623600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:121594000-121612600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:121594200-121627600	Weak transcription	Right Ventricle	heart
10	chr12:121596000-121614800	Weak transcription	Gastric	stomach
11	chr12:121596200-121622200	Weak transcription	Esophagus	oesophagus
12	chr12:121596200-121625600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:121596200-121629000	Weak transcription	Left Ventricle	heart
14	chr12:121596400-121610200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:121596400-121634200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:121597800-121625600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:121598600-121610400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:121599000-121617200	Weak transcription	Fetal Stomach	stomach
19	chr12:121600000-121610200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:121602400-121634600	Weak transcription	Fetal Thymus	thymus
21	chr12:121603800-121623600	Weak transcription	Fetal Intestine Small	intestine
22	chr12:121604000-121615800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:121604200-121613200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:121604200-121613200	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:121604200-121613800	Weak transcription	Adipose Nuclei	Adipose
26	chr12:121604200-121614600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:121604200-121619800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:121604400-121613200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:121604400-121614800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:121604400-121622200	Weak transcription	Lung	lung
31	chr12:121604600-121611400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:121605000-121623400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:121605400-121611200	Weak transcription	Brain Anterior Caudate	brain
34	chr12:121605400-121611200	Weak transcription	Pancreas	Pancrea
35	chr12:121605400-121611200	Weak transcription	Spleen	Spleen
36	chr12:121605400-121612400	Weak transcription	Primary T cells from cord blood	blood
37	chr12:121605400-121613600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:121605400-121615000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:121605600-121610800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr12:121605800-121611200	Weak transcription	Ovary	ovary
41	chr12:121606000-121612600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr12:121606200-121611400	Weak transcription	Brain Angular Gyrus	brain
43	chr12:121606200-121614600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:121606600-121611400	Weak transcription	Liver	Liver
45	chr12:121606600-121614600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:121607600-121610200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:121608000-121610600	Enhancers	HUVEC	blood vessel
48	chr12:121608800-121610200	Enhancers	NHEK	skin
49	chr12:121609000-121610000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr12:121609000-121611400	Weak transcription	Brain Cingulate Gyrus	brain

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