Variant report

Variant	rs17590777
Chromosome Location	chr6:38491231-38491232
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	chr6:38484611..38486326-chr6:38490048..38491576,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12524226	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12525647	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12526648	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12527568	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12528814	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12529497	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12529875	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12529981	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13200466	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13200902	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13203189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13204248	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13205679	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13214868	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13215050	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13217020	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13219695	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13219887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16890768	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs17614684	0.80[CEU][hapmap]
rs2395700	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34222507	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34222775	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34903004	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35509063	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35916993	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4711549	0.88[JPT][hapmap]
rs56867817	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58177962	0.83[ASN][1000 genomes]
rs60138764	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60289806	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67863657	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6909533	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6923594	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6925140	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72853498	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38452400-38496600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:38471600-38493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:38472000-38493800	Weak transcription	Lung	lung
5	chr6:38476600-38499800	Weak transcription	Pancreas	Pancrea
6	chr6:38476800-38498800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:38477800-38498400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:38478000-38494800	Weak transcription	Fetal Kidney	kidney
9	chr6:38479000-38509800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:38482600-38493800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:38483200-38493600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:38483600-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:38485200-38492200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:38485200-38496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:38485400-38493600	Weak transcription	Fetal Intestine Small	intestine
16	chr6:38485400-38493800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:38485400-38500400	Weak transcription	Gastric	stomach
18	chr6:38485600-38493800	Weak transcription	Fetal Intestine Large	intestine
19	chr6:38485800-38493800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:38485800-38495600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:38486000-38493600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:38486400-38493800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:38486400-38495600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:38487000-38492200	Weak transcription	HUVEC	blood vessel
25	chr6:38487000-38493600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:38487000-38518600	Weak transcription	Primary T cells from cord blood	blood
27	chr6:38487400-38493800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:38487600-38493800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:38487600-38493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:38487600-38494000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:38487800-38493800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:38487800-38502600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:38489000-38501000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:38490200-38499600	Weak transcription	Brain Angular Gyrus	brain
35	chr6:38490400-38493800	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:38490400-38493800	Weak transcription	Left Ventricle	heart
37	chr6:38490400-38497800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:38490600-38492200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:38490600-38492400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:38490600-38492600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:38490600-38493600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:38490600-38494000	Weak transcription	Brain Anterior Caudate	brain
43	chr6:38490600-38495800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:38490600-38496200	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:38490600-38503400	Weak transcription	Fetal Lung	lung
46	chr6:38490800-38493400	Weak transcription	Ovary	ovary
47	chr6:38490800-38493800	Weak transcription	Fetal Stomach	stomach
48	chr6:38491000-38491800	Enhancers	Small Intestine	intestine

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