Variant report

Variant	rs10411347
Chromosome Location	chr19:41166954-41166955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41158714..41160657-chr19:41165168..41167753,2	K562	blood:
2	chr19:41166318..41173902-chr19:41219711..41223853,11	K562	blood:
3	chr19:41166820..41170120-chr19:41221252..41223641,4	MCF-7	breast:
4	chr19:41165880..41175149-chr19:41192911..41198858,17	K562	blood:
5	chr19:41161679..41164682-chr19:41165107..41169222,4	K562	blood:

Variant related genes	Relation type
ENSG00000086544	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10409296	0.92[ASN][1000 genomes]
rs10411059	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10421223	0.88[ASN][1000 genomes]
rs2250994	0.89[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2561539	0.90[EUR][1000 genomes]
rs2561542	0.85[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs2561543	0.89[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2561546	0.92[EUR][1000 genomes]
rs2561547	0.88[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2561548	0.92[EUR][1000 genomes]
rs2561551	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2561555	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2561562	0.95[ASN][1000 genomes]
rs2604860	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2604861	0.92[ASN][1000 genomes]
rs2604879	0.81[GIH][hapmap]
rs2604892	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2604900	0.94[EUR][1000 genomes]
rs2604904	0.98[ASN][1000 genomes]
rs2604907	0.98[ASN][1000 genomes]
rs4278858	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67971171	0.97[ASN][1000 genomes]
rs7258709	0.98[ASN][1000 genomes]
rs8110611	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases
9	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv2489	chr19:41145034-41182170	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10411347	SULT2B1	cis	cerebellum	SCAN
rs10411347	IRF2BP1	cis	parietal	SCAN
rs10411347	CLPTM1	cis	parietal	SCAN
rs10411347	KCNN4	cis	cerebellum	SCAN
rs10411347	APOC4	cis	cerebellum	SCAN
rs10411347	NANOS2	cis	cerebellum	SCAN
rs10411347	C19orf54	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41157000-41168200	Weak transcription	Fetal Intestine Small	intestine
2	chr19:41158200-41168400	Weak transcription	Adipose Nuclei	Adipose
3	chr19:41158400-41168800	Weak transcription	Right Atrium	heart
4	chr19:41165600-41168800	Weak transcription	NHDF-Ad	bronchial
5	chr19:41165800-41168600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:41166000-41168200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:41166000-41168400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:41166400-41168000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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