Variant report

Variant	rs12611125
Chromosome Location	chr19:40038291-40038292
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	chr19:40037448..40039461-chr19:40073306..40075141,2	K562	blood:

Variant related genes	Relation type
ENSG00000269188	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12608773	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12609985	0.95[CEU][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs12610740	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12610751	0.95[CEU][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12610833	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12972285	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12972675	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12973775	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12980249	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1368469	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17641650	0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs17795475	0.95[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1836011	0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs34126123	0.84[EUR][1000 genomes]
rs34271968	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34355544	0.85[EUR][1000 genomes]
rs34856311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34885802	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35038530	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35939822	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3746086	0.87[ASN][1000 genomes]
rs4608447	0.80[EUR][1000 genomes]
rs4803258	0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4803259	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55994613	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59485553	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60587381	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67832846	0.85[EUR][1000 genomes]
rs7247184	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7247218	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7257553	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7257904	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258348	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7507648	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12611125	DHX34	cis	cerebellum	SCAN
rs12611125	EID2B	cis	lymphoblastoid	seeQTL
rs12611125	GSK3A	cis	cerebellum	SCAN
rs12611125	SNRPD2	cis	cerebellum	SCAN
rs12611125	CBLC	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40031200-40043600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:40031200-40049600	Weak transcription	Right Atrium	heart
3	chr19:40031400-40042200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:40033600-40042200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:40034200-40038600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr19:40037400-40038400	Enhancers	Placenta	Placenta
7	chr19:40037800-40042400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:40038000-40042000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr19:40038000-40042200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr19:40038000-40042400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:40038200-40038400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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