Variant report

Variant	rs6954401
Chromosome Location	chr7:40687150-40687151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1000013	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1019018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs10256576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10263677	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs10486810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap]
rs10486811	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11973006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap]
rs11974322	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11977013	0.88[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11982075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs17171727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17171730	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17171734	1.00[CEU][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap]
rs17171747	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17171749	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171750	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171753	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1859705	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2329818	1.00[CEU][hapmap];0.94[TSI][hapmap]
rs2329819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap]
rs34523428	1.00[CEU][hapmap];0.94[TSI][hapmap]
rs3919491	1.00[CEU][hapmap]
rs4720370	1.00[CEU][hapmap];0.94[TSI][hapmap]
rs4720371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4723967	0.84[GIH][hapmap];0.94[TSI][hapmap]
rs4723970	0.84[GIH][hapmap];0.94[TSI][hapmap]
rs4723972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs58275184	0.89[EUR][1000 genomes]
rs6462985	1.00[CEU][hapmap]
rs6948724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap]
rs6948900	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6956277	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73310222	0.89[EUR][1000 genomes]
rs73310225	0.87[EUR][1000 genomes]
rs73310227	0.89[EUR][1000 genomes]
rs73310231	0.89[EUR][1000 genomes]
rs73310238	0.89[EUR][1000 genomes]
rs73310243	0.89[EUR][1000 genomes]
rs73310244	0.89[EUR][1000 genomes]
rs7459324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]

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	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv887987	chr7:40505382-40748650	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv830971	chr7:40523075-40700172	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1025605	chr7:40623026-40789063	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv538823	chr7:40623026-40789063	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1019833	chr7:40649369-40767377	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv538824	chr7:40649369-40767377	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv887988	chr7:40685811-40782572	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6954401	POLD2	cis	parietal	SCAN
rs6954401	NOP16	trans	brain	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40680600-40698000	Weak transcription	HSMMtube	muscle
2	chr7:40682200-40690400	Weak transcription	Aorta	Aorta
3	chr7:40683800-40687400	Enhancers	Thymus	Thymus
4	chr7:40686400-40698200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:40687000-40688200	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links