Variant report

Variant	rs7589673
Chromosome Location	chr2:55950628-55950629
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	chr2:55941511..55943436-chr2:55949873..55952751,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10180127	0.81[ASN][1000 genomes]
rs10207466	0.86[ASN][1000 genomes]
rs10460508	0.96[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs10496050	0.92[CEU][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs1084522	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs1084525	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12616629	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1346792	0.88[ASN][1000 genomes]
rs1346793	0.88[ASN][1000 genomes]
rs1579497	0.86[ASN][1000 genomes]
rs17369191	0.92[CEU][hapmap]
rs1823893	0.92[CEU][hapmap]
rs1975484	0.92[CEU][hapmap]
rs1975487	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs2586950	0.90[JPT][hapmap]
rs2586954	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs2586969	0.85[CEU][hapmap]
rs2586970	0.85[CEU][hapmap]
rs2627765	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2627769	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2627773	0.81[CEU][hapmap]
rs2627775	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs2627776	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2868428	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35504023	0.92[CEU][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap]
rs4290693	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs4452190	0.95[ASN][1000 genomes]
rs4672066	0.82[ASN][1000 genomes]
rs62165255	0.80[AMR][1000 genomes]
rs6545506	0.92[CEU][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs6717410	0.88[ASN][1000 genomes]
rs6728604	0.86[ASN][1000 genomes]
rs6748165	0.87[ASN][1000 genomes]
rs706548	0.82[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs7557041	0.86[ASN][1000 genomes]
rs7571327	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs782568	0.96[CEU][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs782572	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs782573	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs782584	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs782585	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs782586	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs782588	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs782590	0.89[CEU][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs782595	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs782599	0.85[CHB][hapmap]
rs782602	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs782606	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs782607	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs782629	0.81[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs782630	0.83[CEU][hapmap]
rs782632	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs782637	0.93[TSI][hapmap]
rs782642	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs782652	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap]
rs809732	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs935177	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv2762645	chr2:55892248-55963418	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised 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
rs7589673	PNPT1	Cis_1M	lymphoblastoid	RTeQTL
rs7589673	PNPT1	cis	lymphoblastoid	seeQTL
rs7589673	PNPT1	cis	cerebellum	SCAN
rs7589673	CCDC104	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55946800-55954400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:55949200-55963200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:55950600-55951000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:55950600-55951200	Enhancers	Esophagus	oesophagus

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