Variant report

Variant	rs1222958
Chromosome Location	chr6:102167208-102167209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10485273	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10872738	0.91[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs10872739	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1222953	0.83[CHB][hapmap]
rs1222955	0.83[CHB][hapmap]
rs1222960	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1337412	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1337415	0.84[CHD][hapmap]
rs1337424	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1415489	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17062395	0.83[CHB][hapmap]
rs1832293	0.91[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1856133	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2065938	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap]
rs2225865	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2518295	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2518303	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2786251	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs2786254	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2852565	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs4839800	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6904687	0.87[CHB][hapmap]
rs6923409	0.95[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs9322602	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9322603	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs9485526	0.95[CEU][hapmap];0.86[CHD][hapmap];0.85[TSI][hapmap]
rs9485530	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9485532	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9498658	0.86[CEU][hapmap]
rs9498659	0.95[CEU][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs9498662	0.95[CEU][hapmap]
rs9498663	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs9498664	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9498667	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3384771	chr6:101996253-102283808	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv1032499	chr6:102069885-102720998	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1016167	chr6:102152010-102198914	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1222958	PRDM13	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:102155200-102170600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:102164800-102168000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr6:102165000-102167600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:102165400-102168600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:102165600-102168000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:102166200-102167800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr6:102166400-102167400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr6:102166400-102167600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr6:102166400-102167800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:102167200-102168400	Weak transcription	H9 Cell Line	embryonic stem cell

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