Variant report

Variant	rs6871116
Chromosome Location	chr5:35924748-35924749
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:35851951..35852800-chr5:35924611..35925609,3	MCF-7	breast:
2	chr5:35777405..35778401-chr5:35924712..35925240,2	K562	blood:
3	chr5:35775517..35778648-chr5:35922425..35925646,3	MCF-7	breast:
4	chr5:35650884..35652138-chr5:35924738..35927702,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168685	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10491434	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1053496	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs11567699	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs11567701	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs11567751	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11949691	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11950831	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955657	1.00[ASN][1000 genomes]
rs11960511	0.83[EUR][1000 genomes]
rs1382347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1494554	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1494571	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs16902573	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17376481	1.00[JPT][hapmap]
rs1833907	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2098706	1.00[CHB][hapmap]
rs2194224	0.80[ASN][1000 genomes]
rs2287900	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2289878	1.00[CHB][hapmap]
rs3194051	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs3734107	1.00[ASN][1000 genomes]
rs3822733	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs3866449	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4024109	0.94[ASN][1000 genomes]
rs4024110	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55654952	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62351973	0.84[EUR][1000 genomes]
rs67207043	0.83[EUR][1000 genomes]
rs6859465	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6868693	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs6873195	0.91[ASN][1000 genomes]
rs6890590	1.00[CHB][hapmap]
rs700179	1.00[JPT][hapmap]
rs72742471	0.83[ASN][1000 genomes]
rs7702828	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7705615	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9764914	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs987107	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs990716	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830261	chr5:35863084-36018048	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1025695	chr5:35902486-36036934	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv4794	chr5:35906690-35934205	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35922800-35924800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:35923200-35925400	Enhancers	NHLF	lung
3	chr5:35923400-35924800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:35923400-35925600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:35924000-35924800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr5:35924000-35925000	Enhancers	Hela-S3	cervix
7	chr5:35924000-35925600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:35924000-35926800	Enhancers	Fetal Thymus	thymus
9	chr5:35924200-35924800	Enhancers	Primary T cells from cord blood	blood
10	chr5:35924200-35924800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr5:35924200-35925000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr5:35924200-35925000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:35924200-35925000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:35924200-35925000	Enhancers	HSMM	muscle
15	chr5:35924200-35925000	Enhancers	NHEK	skin
16	chr5:35924200-35925200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr5:35924200-35925200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:35924200-35925400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:35924200-35925600	Flanking Active TSS	Dnd41	blood
20	chr5:35924200-35925600	Flanking Active TSS	Osteobl	bone
21	chr5:35924200-35931000	Weak transcription	Gastric	stomach
22	chr5:35924400-35924800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr5:35924400-35924800	Bivalent Enhancer	Fetal Brain Female	brain
24	chr5:35924400-35925400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:35924400-35925600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr5:35924400-35925600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr5:35924400-35925600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:35924400-35925600	Flanking Active TSS	Thymus	Thymus
29	chr5:35924400-35925800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:35924400-35926000	Enhancers	Primary hematopoietic stem cells	blood
31	chr5:35924600-35924800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr5:35924600-35924800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:35924600-35924800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:35924600-35924800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:35924600-35924800	Enhancers	Brain Anterior Caudate	brain
36	chr5:35924600-35924800	Enhancers	Brain Cingulate Gyrus	brain
37	chr5:35924600-35924800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr5:35924600-35924800	Flanking Active TSS	HMEC	breast
39	chr5:35924600-35924800	Flanking Active TSS	NH-A	brain
40	chr5:35924600-35925000	Bivalent Enhancer	Brain Germinal Matrix	brain
41	chr5:35924600-35925000	Bivalent Enhancer	Fetal Kidney	kidney
42	chr5:35924600-35925200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:35924600-35925200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:35924600-35925200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:35924600-35925200	Enhancers	HSMMtube	muscle
46	chr5:35924600-35925400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr5:35924600-35925400	Flanking Active TSS	NHDF-Ad	bronchial
48	chr5:35924600-35925600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
49	chr5:35924600-35925600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:35924600-35925600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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