Variant report

Variant	rs2967960
Chromosome Location	chr6:56610769-56610770
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	chr6:56610420..56612281-chr6:56629163..56631061,2	MCF-7	breast:

Extended variants
information (count: 144 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs1024196	0.89[ASN][1000 genomes]
rs10498811	0.82[EUR][1000 genomes]
rs11961141	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961342	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11966986	0.89[ASN][1000 genomes]
rs11967796	0.89[ASN][1000 genomes]
rs11968575	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970648	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13191164	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192037	0.82[EUR][1000 genomes]
rs13192478	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192567	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196211	0.82[EUR][1000 genomes]
rs13198399	0.98[EUR][1000 genomes]
rs13198938	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13203000	0.99[EUR][1000 genomes]
rs13205013	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13206849	0.82[EUR][1000 genomes]
rs13208409	0.81[EUR][1000 genomes]
rs13210876	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213878	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13217390	0.99[EUR][1000 genomes]
rs13219546	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219942	0.97[EUR][1000 genomes]
rs16888070	0.89[ASN][1000 genomes]
rs16888096	0.89[ASN][1000 genomes]
rs16888106	0.89[ASN][1000 genomes]
rs16888118	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888124	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888128	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888130	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888133	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888135	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17684511	0.82[EUR][1000 genomes]
rs17684553	0.83[EUR][1000 genomes]
rs17684571	0.83[EUR][1000 genomes]
rs17751682	0.82[EUR][1000 genomes]
rs17751695	0.82[EUR][1000 genomes]
rs2144407	0.89[ASN][1000 genomes]
rs2180148	0.89[ASN][1000 genomes]
rs2207678	0.89[ASN][1000 genomes]
rs2967963	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002003	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002004	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3002007	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002008	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002009	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3002010	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002011	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34138864	0.82[EUR][1000 genomes]
rs34429594	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34455199	0.99[EUR][1000 genomes]
rs34463732	0.90[EUR][1000 genomes]
rs34465210	0.99[EUR][1000 genomes]
rs34566275	0.99[EUR][1000 genomes]
rs34576803	0.80[EUR][1000 genomes]
rs34587484	0.99[EUR][1000 genomes]
rs34623351	0.99[EUR][1000 genomes]
rs34703847	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34724718	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34803237	0.99[EUR][1000 genomes]
rs34812826	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824960	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34832779	0.98[EUR][1000 genomes]
rs35089136	1.00[ASN][1000 genomes]
rs35206656	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35326806	0.97[EUR][1000 genomes]
rs35408048	0.82[EUR][1000 genomes]
rs35494794	0.97[EUR][1000 genomes]
rs35619924	0.82[EUR][1000 genomes]
rs35637749	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35668437	0.82[EUR][1000 genomes]
rs35687635	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35876418	0.99[EUR][1000 genomes]
rs35920751	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36068365	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4072271	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4073960	0.84[AFR][1000 genomes]
rs4074101	0.82[EUR][1000 genomes]
rs4074102	0.82[EUR][1000 genomes]
rs41267673	0.89[ASN][1000 genomes]
rs41267675	0.99[EUR][1000 genomes]
rs41271876	0.89[ASN][1000 genomes]
rs41271878	0.89[ASN][1000 genomes]
rs4133076	0.89[ASN][1000 genomes]
rs4275049	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45553042	0.89[ASN][1000 genomes]
rs4574644	1.00[ASN][1000 genomes]
rs4640889	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5024547	0.82[EUR][1000 genomes]
rs55742092	0.82[EUR][1000 genomes]
rs56094263	1.00[ASN][1000 genomes]
rs56101897	0.82[EUR][1000 genomes]
rs56196625	0.89[ASN][1000 genomes]
rs57289287	0.89[ASN][1000 genomes]
rs57350484	0.89[ASN][1000 genomes]
rs57392123	0.89[ASN][1000 genomes]
rs57488435	0.89[ASN][1000 genomes]
rs58565063	0.89[ASN][1000 genomes]
rs59073430	0.89[ASN][1000 genomes]
rs59085778	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59162324	1.00[ASN][1000 genomes]
rs59247267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59772940	0.89[ASN][1000 genomes]
rs59889120	0.89[ASN][1000 genomes]
rs60360551	0.89[ASN][1000 genomes]
rs60498201	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412526	0.82[EUR][1000 genomes]
rs62412528	0.82[EUR][1000 genomes]
rs62412531	0.82[EUR][1000 genomes]
rs62412532	0.82[EUR][1000 genomes]
rs62412544	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62412556	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6459167	0.89[ASN][1000 genomes]
rs6459168	0.89[ASN][1000 genomes]
rs6900572	0.89[ASN][1000 genomes]
rs6901176	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6903815	0.89[ASN][1000 genomes]
rs6904535	0.83[AMR][1000 genomes]
rs6916813	0.89[ASN][1000 genomes]
rs6924375	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926134	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938003	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6941626	0.89[ASN][1000 genomes]
rs71564848	0.80[EUR][1000 genomes]
rs71564849	0.83[EUR][1000 genomes]
rs73746926	0.89[ASN][1000 genomes]
rs73746929	0.89[ASN][1000 genomes]
rs73746930	0.89[ASN][1000 genomes]
rs73746931	0.89[ASN][1000 genomes]
rs7749100	0.89[ASN][1000 genomes]
rs7749437	0.89[ASN][1000 genomes]
rs7759479	0.89[ASN][1000 genomes]
rs7760503	0.89[ASN][1000 genomes]
rs7760542	0.89[ASN][1000 genomes]
rs7761027	0.89[ASN][1000 genomes]
rs7767128	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7775134	0.89[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56582600-56611600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:56592800-56611800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:56593200-56621200	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:56605000-56613400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr6:56605600-56611600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:56605600-56614600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:56606600-56614000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr6:56606600-56617600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:56606800-56611400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:56606800-56612400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:56607000-56612000	Weak transcription	Fetal Brain Female	brain
12	chr6:56607200-56610800	Weak transcription	Placenta	Placenta
13	chr6:56607200-56611600	Weak transcription	Left Ventricle	heart
14	chr6:56607200-56611600	Weak transcription	Right Atrium	heart
15	chr6:56607200-56611600	Weak transcription	Right Ventricle	heart
16	chr6:56607200-56614200	Weak transcription	Gastric	stomach
17	chr6:56607200-56618200	Weak transcription	Brain Germinal Matrix	brain
18	chr6:56607400-56611600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:56607600-56611600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:56607600-56611600	Weak transcription	HSMMtube	muscle
21	chr6:56607600-56612600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:56607600-56620600	Weak transcription	Fetal Intestine Small	intestine
23	chr6:56607800-56611600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:56607800-56611600	Enhancers	GM12878-XiMat	blood
25	chr6:56608000-56611600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:56608000-56613800	Weak transcription	NH-A	brain
27	chr6:56608200-56614600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:56608200-56621000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:56608400-56611600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:56608400-56614200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:56608400-56614600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:56608600-56611000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:56608600-56611600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:56608600-56611600	Weak transcription	HepG2	liver
35	chr6:56608600-56611600	Weak transcription	Osteobl	bone
36	chr6:56608600-56614400	Weak transcription	NHDF-Ad	bronchial
37	chr6:56608600-56618000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:56609000-56612400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr6:56609200-56610800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr6:56609200-56612600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:56609200-56617600	Enhancers	HMEC	breast
42	chr6:56609200-56619200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:56609400-56611600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:56609400-56611600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:56609400-56611600	Enhancers	NHEK	skin
46	chr6:56609600-56610800	Weak transcription	Psoas Muscle	Psoas
47	chr6:56609600-56611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr6:56609600-56611600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:56609600-56611600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr6:56609600-56612000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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