Variant report

Variant	rs1469981
Chromosome Location	chr2:86239772-86239773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86226779..86229751-chr2:86239131..86240929,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10168997	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11127012	0.93[CEU][hapmap]
rs11885520	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11886175	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11895453	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11903682	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12124	0.85[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13390107	0.86[AMR][1000 genomes]
rs1469982	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17579744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1978842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278532	0.90[JPT][hapmap]
rs311587	0.87[AFR][1000 genomes]
rs3731822	0.85[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3770064	0.84[CHD][hapmap]
rs3770086	0.90[JPT][hapmap]
rs3770088	0.81[JPT][hapmap]
rs3770091	0.90[JPT][hapmap]
rs57339071	0.86[AMR][1000 genomes]
rs57361751	0.83[ASN][1000 genomes]
rs57405155	0.83[ASN][1000 genomes]
rs58077381	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58913632	0.83[ASN][1000 genomes]
rs6707736	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6708805	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6749218	0.86[AMR][1000 genomes]
rs6752561	0.84[AMR][1000 genomes]
rs72847838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72847843	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72847845	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72847853	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7569121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7599498	1.00[CEU][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9679308	1.00[AMR][1000 genomes];0.88[EUR][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	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1469981	POLR1A	cis	parietal	SCAN
rs1469981	POLR1A	cis	multi-tissue	Pritchard
rs1469981	MRPL35	cis	parietal	SCAN
rs1469981	MRPL35	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86238200-86239800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:86238400-86239800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:86238400-86239800	Enhancers	Placenta	Placenta
4	chr2:86238400-86240200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:86238400-86240200	Enhancers	Fetal Muscle Leg	muscle
6	chr2:86238800-86239800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:86238800-86240200	Enhancers	Left Ventricle	heart
8	chr2:86239200-86240400	Enhancers	Fetal Muscle Trunk	muscle
9	chr2:86239200-86240600	Enhancers	Primary B cells from peripheral blood	blood
10	chr2:86239400-86240200	Enhancers	Primary B cells from cord blood	blood
11	chr2:86239400-86240400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr2:86239400-86240600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:86239600-86239800	Enhancers	Psoas Muscle	Psoas
14	chr2:86239600-86244000	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links