Variant report

Variant	rs1990250
Chromosome Location	chr4:110770124-110770125
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110733962..110737774-chr4:110769396..110773000,3	K562	blood:
2	chr4:110764137..110765639-chr4:110769412..110771941,2	K562	blood:

Variant related genes	Relation type
ENSG00000109534	Chromatin interaction
ENSG00000272795	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10365	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11721403	0.83[ASW][hapmap]
rs11724973	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs11733397	0.82[CEU][hapmap]
rs11930428	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11937249	0.83[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12642452	0.85[AMR][1000 genomes]
rs13107617	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13128301	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2347129	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3188897	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35386791	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35646628	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4698797	0.84[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6533470	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs6814789	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6827802	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7438763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764205	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7654660	0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7664699	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7679303	0.84[CEU][hapmap];0.86[MEX][hapmap]

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	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1990250	CYP2U1	cis	parietal	SCAN
rs1990250	RRH	cis	cerebellum	SCAN
rs1990250	RRH	cis	parietal	SCAN
rs1990250	LRIT3	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110737600-110770600	Weak transcription	Aorta	Aorta
2	chr4:110744400-110774400	Weak transcription	Psoas Muscle	Psoas
3	chr4:110744600-110773200	Weak transcription	Primary T cells from cord blood	blood
4	chr4:110757800-110772800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:110763400-110771800	Weak transcription	Pancreas	Pancrea
6	chr4:110769200-110770600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:110769400-110770200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr4:110769600-110771800	Weak transcription	Liver	Liver
9	chr4:110770000-110770600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links