Variant report

Variant	rs2842514
Chromosome Location	chr6:37912482-37912483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37786296..37788454-chr6:37912478..37914475,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs11759458	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11964613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11964671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11968604	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11970017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11970145	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13198459	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13203867	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13205214	1.00[JPT][hapmap]
rs13207526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13210967	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13211881	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13217630	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13218158	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13219500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16890185	1.00[JPT][hapmap];0.80[YRI][hapmap]
rs16890194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16890301	0.88[CEU][hapmap]
rs16890365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2395689	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs2453882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2645115	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2645118	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2645121	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2645123	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2645126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28385568	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2842498	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2842499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842511	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2842512	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2842513	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs33997846	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34011349	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34054102	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34449592	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34611895	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34618835	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34634043	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34745343	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35051126	0.91[EUR][1000 genomes]
rs35248825	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35330991	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35465740	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35575717	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35609407	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35653300	0.87[EUR][1000 genomes]
rs35953900	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35955196	0.83[EUR][1000 genomes]
rs36069529	0.83[EUR][1000 genomes]
rs4394213	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56391784	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56678832	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6458037	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6908106	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6908761	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6910715	0.82[JPT][hapmap]
rs6910837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6911481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6912250	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6916057	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6916535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6917208	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6917736	0.87[EUR][1000 genomes]
rs6918802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6919884	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6923132	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6923254	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6925563	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6933547	1.00[YRI][hapmap]
rs6936260	0.82[JPT][hapmap]
rs6940491	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs71569395	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71569397	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7742379	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7747538	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7750445	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7757560	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7760770	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7762052	0.82[JPT][hapmap]
rs7776025	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296236	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	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
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:37880200-37930000	Weak transcription	Thymus	Thymus
3	chr6:37884800-37917000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr6:37887600-37933200	Weak transcription	NHDF-Ad	bronchial
5	chr6:37892600-37928800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:37896800-37929000	Weak transcription	Esophagus	oesophagus
7	chr6:37898200-37913800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:37901000-37915400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:37902200-37913600	Weak transcription	HepG2	liver
10	chr6:37904800-37920400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:37904800-37920400	Weak transcription	Small Intestine	intestine
12	chr6:37904800-37933400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:37905000-37919600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:37905800-37916200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:37905800-37916600	Weak transcription	Dnd41	blood
16	chr6:37905800-37924000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr6:37907000-37921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:37907000-37926600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:37908200-37913600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:37908600-37920400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:37909400-37912800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr6:37909600-37912800	Weak transcription	Fetal Heart	heart
23	chr6:37909600-37914400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:37909800-37917400	Weak transcription	Ovary	ovary
25	chr6:37910000-37912600	Weak transcription	Psoas Muscle	Psoas
26	chr6:37910000-37913200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:37910000-37913800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:37910000-37913800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:37910000-37913800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:37910000-37922600	Weak transcription	Right Ventricle	heart
31	chr6:37910800-37912600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:37910800-37914000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:37910800-37914000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:37910800-37914200	Weak transcription	Fetal Brain Male	brain
35	chr6:37911000-37913600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:37911000-37914000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:37911000-37919600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:37911000-37933200	Weak transcription	NHEK	skin
39	chr6:37911200-37912800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr6:37911200-37913800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:37911200-37913800	Weak transcription	Stomach Mucosa	stomach
42	chr6:37911200-37914000	Weak transcription	Brain Anterior Caudate	brain
43	chr6:37911400-37913600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr6:37911400-37915400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:37911400-37917000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:37911400-37919600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr6:37911400-37919800	Weak transcription	Adipose Nuclei	Adipose
48	chr6:37911400-37922600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:37911600-37912800	Weak transcription	Brain Angular Gyrus	brain
50	chr6:37911600-37914000	Weak transcription	Brain Substantia Nigra	brain

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