Variant report

Variant	rs9304578
Chromosome Location	chr19:39250337-39250338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10405232	1.00[YRI][hapmap]
rs10405261	1.00[YRI][hapmap]
rs10407371	0.95[EUR][1000 genomes]
rs10413936	1.00[YRI][hapmap]
rs10415219	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs10416718	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10418728	0.94[EUR][1000 genomes]
rs10421087	1.00[YRI][hapmap]
rs10421560	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs11083475	0.92[CEU][hapmap]
rs11673323	0.92[EUR][1000 genomes]
rs12460849	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs12462270	0.91[CEU][hapmap]
rs13344413	0.86[ASW][hapmap];0.85[CEU][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs16972767	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs2279144	0.89[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap]
rs2287734	1.00[YRI][hapmap]
rs2303040	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs3745859	0.92[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap]
rs3786835	0.92[CEU][hapmap]
rs3786839	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs3786845	0.92[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap]
rs3786851	0.92[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap]
rs4802887	0.86[ASW][hapmap]
rs55873140	0.86[AMR][1000 genomes]
rs55923191	0.87[EUR][1000 genomes]
rs55945853	0.82[EUR][1000 genomes]
rs56172450	0.86[EUR][1000 genomes]
rs62120083	0.83[EUR][1000 genomes]
rs62120087	0.83[EUR][1000 genomes]
rs7251903	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs7254100	0.91[CEU][hapmap]
rs8107416	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs883433	0.92[CEU][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap]
rs979971	0.92[CEU][hapmap];0.91[TSI][hapmap]
rs979972	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
5	nsv1064688	chr19:39249059-39291526	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv1061904	chr19:39249692-39302843	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
7	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9304578	ERCC1	cis	cerebellum	SCAN
rs9304578	PSG3	cis	parietal	SCAN
rs9304578	LGALS17A	cis	cerebellum	SCAN
rs9304578	MEGF8	cis	parietal	SCAN
rs9304578	ZNF526	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39246400-39270800	Weak transcription	K562	blood
2	chr19:39249000-39252200	Enhancers	HepG2	liver
3	chr19:39249000-39252800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:39249600-39250800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:39249800-39250400	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr19:39249800-39250600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr19:39249800-39251400	Enhancers	Duodenum Mucosa	Duodenum
8	chr19:39249800-39251400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr19:39249800-39252400	Enhancers	Fetal Intestine Small	intestine
10	chr19:39250000-39250800	Enhancers	Spleen	Spleen
11	chr19:39250200-39250400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr19:39250200-39250600	Weak transcription	Liver	Liver
13	chr19:39250200-39250600	Enhancers	Brain Hippocampus Middle	brain
14	chr19:39250200-39250600	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr19:39250200-39253800	Enhancers	Fetal Intestine Large	intestine

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