Variant report

Variant	rs431116
Chromosome Location	chr6:75946422-75946423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:75942897..75944973-chr6:75945233..75947234,2	MCF-7	breast:
2	chr6:75932967..75935533-chr6:75943736..75947301,4	K562	blood:
3	chr6:75946301..75951139-chr6:75992372..75997214,5	K562	blood:
4	chr6:75945623..75947562-chr6:76246342..76248731,3	K562	blood:
5	chr6:75937140..75939759-chr6:75945754..75948396,2	MCF-7	breast:
6	chr6:75943060..75944585-chr6:75945080..75947516,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225793	Chromatin interaction
ENSG00000112697	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1203210	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1203215	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12176508	0.86[EUR][1000 genomes]
rs12198145	0.90[CEU][hapmap]
rs12215389	0.90[CEU][hapmap];1.00[GIH][hapmap]
rs1407733	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1407734	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1474847	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs171261	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs171264	0.90[CEU][hapmap]
rs173274	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs187067	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs1967709	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1998454	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs240363	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs240365	0.94[EUR][1000 genomes]
rs240366	0.90[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes]
rs240370	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs240394	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs240395	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs240399	0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs240408	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs240411	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs240414	0.90[CEU][hapmap];1.00[GIH][hapmap]
rs240417	0.90[CEU][hapmap]
rs240418	0.81[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs240420	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs240421	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs240422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs240433	1.00[CEU][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs2748254	0.82[GIH][hapmap]
rs3756791	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3777507	0.90[CEU][hapmap]
rs3777510	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs409536	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436898	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511970	0.90[CEU][hapmap]
rs57613317	0.83[ASN][1000 genomes]
rs588691	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs601846	0.94[EUR][1000 genomes]
rs656182	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450107	0.83[ASN][1000 genomes]
rs743003	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs743004	0.90[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs743005	0.94[EUR][1000 genomes]
rs7768671	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs910523	1.00[CEU][hapmap];0.82[CHD][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs9293997	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs9443160	1.00[CEU][hapmap];0.90[EUR][1000 genomes]

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	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75917600-75946600	Weak transcription	Lung	lung
2	chr6:75922600-75947000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:75934000-75948800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:75934600-75946800	Weak transcription	Fetal Lung	lung
5	chr6:75934600-75948600	Weak transcription	Pancreas	Pancrea
6	chr6:75935000-75947200	Weak transcription	HepG2	liver
7	chr6:75936400-75946800	Weak transcription	HUVEC	blood vessel
8	chr6:75940400-75946800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:75940400-75947600	Weak transcription	Fetal Intestine Small	intestine
10	chr6:75940400-75948000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:75940400-75952600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:75940600-75946600	Weak transcription	NHEK	skin
13	chr6:75940800-75946800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:75941200-75948600	Weak transcription	Esophagus	oesophagus
15	chr6:75941400-75946800	Weak transcription	NHDF-Ad	bronchial
16	chr6:75941600-75946600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:75941600-75948800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:75942400-75946800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:75943000-75946600	Weak transcription	GM12878-XiMat	blood
20	chr6:75943200-75952000	Weak transcription	Psoas Muscle	Psoas
21	chr6:75943600-75948200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:75944000-75946600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:75944000-75950600	Weak transcription	Hela-S3	cervix
24	chr6:75944200-75947000	Weak transcription	Colonic Mucosa	Colon
25	chr6:75944200-75950800	Weak transcription	NHLF	lung
26	chr6:75944200-75953000	Weak transcription	Stomach Mucosa	stomach
27	chr6:75944400-75946600	Weak transcription	Fetal Brain Male	brain
28	chr6:75944400-75946800	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:75944400-75947200	Weak transcription	Small Intestine	intestine
30	chr6:75944400-75950400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:75944400-75952800	Weak transcription	Aorta	Aorta
32	chr6:75944400-75952800	Weak transcription	Brain Angular Gyrus	brain
33	chr6:75944400-75952800	Weak transcription	Ovary	ovary
34	chr6:75944600-75948600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:75944800-75946600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:75944800-75946600	Weak transcription	Placenta	Placenta
37	chr6:75944800-75946600	Weak transcription	Dnd41	blood
38	chr6:75945000-75946600	Weak transcription	Brain Substantia Nigra	brain
39	chr6:75945000-75948800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr6:75945200-75946800	Weak transcription	Fetal Heart	heart
41	chr6:75945200-75948600	Weak transcription	Spleen	Spleen
42	chr6:75945200-75949400	Strong transcription	Primary T cells from cord blood	blood
43	chr6:75945200-75950600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:75945400-75947000	Weak transcription	K562	blood
45	chr6:75945400-75948000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:75945400-75950800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr6:75945400-75951400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:75945400-75951400	Strong transcription	Fetal Thymus	thymus
49	chr6:75945600-75946600	Weak transcription	Brain Germinal Matrix	brain
50	chr6:75945600-75947400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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