Variant report

Variant	rs2474921
Chromosome Location	chr6:71552042-71552043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:71545104..71548223-chr6:71550454..71553252,3	MCF-7	breast:
2	chr6:71546521..71548760-chr6:71551365..71554276,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13197338	0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13198627	0.91[ASN][1000 genomes]
rs13202113	0.92[ASN][1000 genomes]
rs13203355	0.94[ASN][1000 genomes]
rs13212771	0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1333968	0.86[GIH][hapmap]
rs2038477	0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap]
rs2460692	0.84[EUR][1000 genomes]
rs2474914	0.82[CEU][hapmap];0.90[MKK][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2474915	0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap]
rs2504748	0.94[CHB][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes]
rs2504750	0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs2504751	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2504752	0.94[CHB][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes]
rs34336229	0.94[ASN][1000 genomes]
rs4706459	0.91[EUR][1000 genomes]
rs4707848	0.91[EUR][1000 genomes]
rs483894	0.83[JPT][hapmap]
rs6927575	0.84[GIH][hapmap]
rs9354939	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9354940	0.94[CEU][hapmap];1.00[GIH][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9680	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][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	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	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	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
rs2474921	BAI3	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71474600-71568800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:71492400-71563600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:71506800-71570600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:71511600-71554600	Weak transcription	Dnd41	blood
5	chr6:71516400-71562200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:71516400-71567600	Weak transcription	Pancreas	Pancrea
7	chr6:71516600-71567600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:71518400-71552400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:71522000-71558200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:71531200-71571000	Weak transcription	Stomach Mucosa	stomach
11	chr6:71532400-71557200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:71533000-71567600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:71533200-71557000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr6:71534000-71563200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:71534800-71567600	Weak transcription	Aorta	Aorta
16	chr6:71537200-71556000	Weak transcription	Right Ventricle	heart
17	chr6:71537600-71574200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:71538800-71553200	Weak transcription	Gastric	stomach
19	chr6:71538800-71555400	Weak transcription	Esophagus	oesophagus
20	chr6:71539200-71556000	Weak transcription	Fetal Intestine Small	intestine
21	chr6:71543800-71562200	Weak transcription	Fetal Thymus	thymus
22	chr6:71544400-71562200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:71544400-71562200	Weak transcription	Adipose Nuclei	Adipose
24	chr6:71544400-71567200	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:71544400-71568800	Weak transcription	HSMMtube	muscle
26	chr6:71544400-71569800	Weak transcription	Placenta	Placenta
27	chr6:71544600-71566600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:71545400-71566200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr6:71545400-71572200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:71546000-71557400	Weak transcription	Lung	lung
31	chr6:71546200-71567000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:71547000-71562200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:71547200-71567000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:71547200-71567600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:71547800-71567200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:71548200-71556000	Weak transcription	Fetal Stomach	stomach
37	chr6:71548600-71567600	Weak transcription	Left Ventricle	heart
38	chr6:71549000-71567400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr6:71549200-71567200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:71549200-71570000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:71549400-71558200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:71549800-71553200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:71549800-71555400	Weak transcription	Psoas Muscle	Psoas
44	chr6:71549800-71555600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:71549800-71557200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:71549800-71568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:71549800-71573000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:71550000-71555600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:71550000-71575400	Weak transcription	Ovary	ovary
50	chr6:71550200-71562200	Weak transcription	Primary T cells fromperipheralblood	blood

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