Variant report

Variant	rs746121
Chromosome Location	chr6:71574795-71574796
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2038477	0.93[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.83[MKK][hapmap];0.84[EUR][1000 genomes]
rs2460692	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2460699	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2474914	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]
rs2474915	0.89[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2474916	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2504748	0.81[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap];0.90[ASN][1000 genomes]
rs2504749	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504750	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2504752	0.81[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2504753	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3734371	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3734372	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs483894	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs576516	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

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
rs746121	BAI3	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71550000-71575400	Weak transcription	Ovary	ovary
2	chr6:71558800-71575000	Weak transcription	HUVEC	blood vessel
3	chr6:71564000-71575800	Weak transcription	Right Ventricle	heart
4	chr6:71569000-71575600	Weak transcription	Gastric	stomach
5	chr6:71571400-71575000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:71571600-71576400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:71571600-71584000	Weak transcription	Pancreas	Pancrea
8	chr6:71572000-71575800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:71572800-71574800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:71572800-71574800	Enhancers	Thymus	Thymus
11	chr6:71573400-71574800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:71573400-71574800	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:71573600-71574800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr6:71574000-71574800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr6:71574000-71574800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:71574000-71574800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:71574600-71574800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr6:71574600-71574800	Enhancers	Primary hematopoietic stem cells	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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