Variant report

Variant	rs10002931
Chromosome Location	chr4:15396759-15396760
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	chr4:15386891..15389601-chr4:15395549..15397973,3	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10003338	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10032941	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10212844	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10212901	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10213628	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1024758	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs1048037	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10488970	0.84[EUR][1000 genomes]
rs11934015	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11937671	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12233742	0.84[EUR][1000 genomes]
rs13106702	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13114788	0.84[EUR][1000 genomes]
rs13123785	0.80[CEU][hapmap]
rs13124324	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13124984	0.83[EUR][1000 genomes]
rs13131227	0.86[CHD][hapmap]
rs13132007	0.84[EUR][1000 genomes]
rs13132446	0.84[EUR][1000 genomes]
rs13132604	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs13138481	0.85[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs16891929	0.82[EUR][1000 genomes]
rs16891934	0.82[EUR][1000 genomes]
rs1990524	0.84[EUR][1000 genomes]
rs2160043	0.84[JPT][hapmap]
rs2160046	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2192355	0.84[EUR][1000 genomes]
rs2192363	0.85[ASN][1000 genomes]
rs2192364	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2215810	0.85[ASN][1000 genomes]
rs28376639	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2872704	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34028526	0.84[EUR][1000 genomes]
rs34351987	0.84[EUR][1000 genomes]
rs34352292	0.84[EUR][1000 genomes]
rs35866305	0.84[EUR][1000 genomes]
rs35971217	0.84[EUR][1000 genomes]
rs3797006	0.81[CEU][hapmap]
rs3822296	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4140932	0.85[ASN][1000 genomes]
rs59684117	0.84[EUR][1000 genomes]
rs61240629	0.84[EUR][1000 genomes]
rs62289285	0.84[EUR][1000 genomes]
rs6449138	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6828721	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6855244	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71601473	0.84[EUR][1000 genomes]
rs7442554	0.83[EUR][1000 genomes]
rs7661287	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7681816	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7687272	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7690471	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7697778	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs973629	0.85[ASN][1000 genomes]
rs9991652	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10002931	SLC39A8	trans	cerebellum	SCAN
rs10002931	HS3ST1	cis	parietal	SCAN
rs10002931	CPEB2	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15378600-15401200	Weak transcription	Primary B cells from cord blood	blood
2	chr4:15384400-15402000	Weak transcription	Fetal Lung	lung
3	chr4:15388200-15400000	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:15388400-15401800	Weak transcription	Fetal Stomach	stomach
5	chr4:15394200-15397600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:15394200-15397800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:15394200-15400000	Weak transcription	Lung	lung
8	chr4:15394400-15401600	Weak transcription	HSMMtube	muscle
9	chr4:15394400-15402400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:15396000-15397800	Weak transcription	Aorta	Aorta
11	chr4:15396000-15398000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:15396400-15396800	Weak transcription	Right Atrium	heart
13	chr4:15396600-15397600	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links