Variant report

Variant	rs6941089
Chromosome Location	chr6:121653046-121653047
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	chr6:121622881..121625518-chr6:121651420..121653237,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1273745	0.85[CHB][hapmap]
rs1273748	0.85[CHB][hapmap]
rs17083373	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083415	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17083440	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17154	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1776817	0.85[CHB][hapmap]
rs2133990	1.00[ASN][1000 genomes]
rs2186097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2455056	0.85[CHB][hapmap]
rs2892765	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2995680	0.85[CHB][hapmap]
rs4072142	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132315	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4305755	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4371872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4584021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55799213	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55975505	0.94[AFR][1000 genomes]
rs55983388	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56000113	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56927912	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58124381	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61047660	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61293964	1.00[ASN][1000 genomes]
rs6903467	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6919916	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6920055	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6925413	1.00[ASN][1000 genomes]
rs73526695	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73528541	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73768932	1.00[ASN][1000 genomes]
rs73768938	1.00[ASN][1000 genomes]
rs7451033	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7741356	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7742071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743455	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7744891	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7749984	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7751636	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755977	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757350	0.89[EUR][1000 genomes]
rs7759798	1.00[ASN][1000 genomes]
rs7761551	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7767417	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768813	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs785407	1.00[CEU][hapmap]
rs9490148	1.00[ASN][1000 genomes]
rs9490164	0.92[TSI][hapmap]
rs975679	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023384	chr6:121235867-121683448	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv530527	chr6:121298528-121789855	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830789	chr6:121581450-121732320	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121586400-121655000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:121588400-121655200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:121589000-121654200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:121589200-121655000	Weak transcription	Fetal Stomach	stomach
5	chr6:121594200-121654800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:121606600-121655000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:121611200-121655000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:121615600-121655000	Weak transcription	Pancreas	Pancrea
9	chr6:121616200-121655000	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:121622200-121654600	Weak transcription	Fetal Thymus	thymus
11	chr6:121622600-121655000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:121622800-121654800	Weak transcription	Brain Germinal Matrix	brain
13	chr6:121632000-121654200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:121632200-121653800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr6:121632200-121654200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:121632200-121655000	Weak transcription	HSMM	muscle
17	chr6:121632400-121654600	Weak transcription	HMEC	breast
18	chr6:121632800-121655000	Weak transcription	Lung	lung
19	chr6:121634600-121654800	Weak transcription	Fetal Brain Male	brain
20	chr6:121635000-121653800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:121635200-121655200	Weak transcription	Aorta	Aorta
22	chr6:121636000-121654800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:121636200-121654200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr6:121636600-121655000	Weak transcription	Esophagus	oesophagus
25	chr6:121636800-121654800	Weak transcription	Placenta	Placenta
26	chr6:121637000-121655000	Weak transcription	Fetal Intestine Small	intestine
27	chr6:121637200-121654000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:121637200-121655000	Weak transcription	Liver	Liver
29	chr6:121638200-121655200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:121638400-121654400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr6:121638800-121654400	Weak transcription	Primary T cells from cord blood	blood
32	chr6:121639600-121654400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:121640600-121654200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:121640600-121654200	Weak transcription	Fetal Intestine Large	intestine
35	chr6:121640600-121654800	Weak transcription	Brain Angular Gyrus	brain
36	chr6:121640600-121655200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:121640600-121655200	Weak transcription	Adipose Nuclei	Adipose
38	chr6:121640600-121655200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:121640600-121655200	Weak transcription	NH-A	brain
40	chr6:121640600-121655400	Weak transcription	Fetal Heart	heart
41	chr6:121640800-121654200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:121640800-121654600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:121640800-121654600	Weak transcription	Small Intestine	intestine
44	chr6:121640800-121654800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:121640800-121655000	Weak transcription	Brain Anterior Caudate	brain
46	chr6:121642800-121654600	Weak transcription	Primary B cells from cord blood	blood
47	chr6:121642800-121655000	Weak transcription	Left Ventricle	heart
48	chr6:121643000-121653600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:121643000-121655000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:121648800-121653400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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