Variant report

Variant	rs2474914
Chromosome Location	chr6:71568417-71568418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10498876	0.81[GIH][hapmap]
rs10945246	0.81[GIH][hapmap]
rs12215467	0.81[GIH][hapmap]
rs12215835	0.81[GIH][hapmap]
rs1333967	0.81[GIH][hapmap]
rs17763077	0.85[LWK][hapmap];0.82[YRI][hapmap]
rs2038477	0.81[GIH][hapmap];0.89[JPT][hapmap]
rs2460689	0.81[GIH][hapmap]
rs2460692	0.83[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2460699	0.84[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2474913	0.81[GIH][hapmap]
rs2474915	0.81[GIH][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2474916	0.85[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2474921	0.82[CEU][hapmap];0.90[MKK][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2504748	0.81[CEU][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2504749	0.90[ASN][1000 genomes]
rs2504750	0.89[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2504752	0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs2504753	0.80[ASN][1000 genomes]
rs2504756	0.86[GIH][hapmap]
rs3734371	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3734372	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4613778	0.81[GIH][hapmap]
rs4706462	0.81[GIH][hapmap]
rs4706464	0.81[GIH][hapmap]
rs4707847	0.81[GIH][hapmap]
rs4707855	0.81[GIH][hapmap]
rs483894	0.85[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs576516	0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746121	0.85[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7771674	0.81[GIH][hapmap]
rs781969	0.81[GIH][hapmap]
rs781987	0.81[GIH][hapmap]
rs9354939	0.82[CEU][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap]
rs9354940	1.00[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9455215	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2474914	BAI3	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71474600-71568800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:71506800-71570600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:71531200-71571000	Weak transcription	Stomach Mucosa	stomach
4	chr6:71537600-71574200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:71544400-71568800	Weak transcription	HSMMtube	muscle
6	chr6:71544400-71569800	Weak transcription	Placenta	Placenta
7	chr6:71545400-71572200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr6:71549200-71570000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:71549800-71568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:71549800-71573000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:71550000-71575400	Weak transcription	Ovary	ovary
12	chr6:71550600-71573000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:71551000-71571400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:71551200-71568600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:71551200-71570200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:71551200-71570400	Weak transcription	Fetal Brain Female	brain
17	chr6:71552400-71574200	Weak transcription	HSMM	muscle
18	chr6:71554400-71572800	Weak transcription	Thymus	Thymus
19	chr6:71554400-71572800	Weak transcription	Osteobl	bone
20	chr6:71554400-71574400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:71554600-71572800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:71555600-71570200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:71556200-71570400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:71556400-71568600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:71556600-71568600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:71556600-71568800	Weak transcription	Esophagus	oesophagus
27	chr6:71556600-71571400	Weak transcription	Psoas Muscle	Psoas
28	chr6:71556600-71574400	Weak transcription	Fetal Intestine Small	intestine
29	chr6:71557000-71572800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:71557200-71569600	Weak transcription	Fetal Brain Male	brain
31	chr6:71557200-71572200	Weak transcription	Fetal Heart	heart
32	chr6:71557400-71568600	Weak transcription	Primary T cells from cord blood	blood
33	chr6:71557600-71569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:71557600-71570000	Weak transcription	Small Intestine	intestine
35	chr6:71557800-71569800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:71558800-71575000	Weak transcription	HUVEC	blood vessel
37	chr6:71559000-71569800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:71559000-71573800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:71559400-71573800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:71560600-71574200	Weak transcription	Brain Germinal Matrix	brain
41	chr6:71560800-71570000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:71561000-71569800	Weak transcription	Fetal Lung	lung
43	chr6:71561200-71569800	Weak transcription	NHLF	lung
44	chr6:71561200-71573000	Weak transcription	Brain Anterior Caudate	brain
45	chr6:71561200-71573400	Weak transcription	HMEC	breast
46	chr6:71561600-71574000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:71562200-71568600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:71563400-71573600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:71563800-71571600	Weak transcription	HepG2	liver
50	chr6:71564000-71570000	Weak transcription	Primary hematopoietic stem cells	blood

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