Variant report

Variant	rs349032
Chromosome Location	chr19:44317360-44317361
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	chr19:44317183..44320070-chr19:44329889..44332057,2	K562	blood:
2	chr19:44316369..44317952-chr19:44320747..44323112,2	K562	blood:

Variant related genes	Relation type
ENSG00000167637	Chromatin interaction
ENSG00000159871	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1036246	0.95[ASN][1000 genomes]
rs10405318	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10408461	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10412955	0.95[ASN][1000 genomes]
rs10415344	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs10416116	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10421861	0.84[GIH][hapmap]
rs10500286	0.92[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10500287	0.92[CEU][hapmap];0.93[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs11878787	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11879541	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11880651	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12462507	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12608578	0.96[ASN][1000 genomes]
rs13344589	0.93[ASN][1000 genomes]
rs1549953	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1549954	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1549955	0.95[ASN][1000 genomes]
rs1549956	0.95[ASN][1000 genomes]
rs1549957	0.95[ASN][1000 genomes]
rs1549959	0.95[ASN][1000 genomes]
rs1565057	0.92[CEU][hapmap];0.93[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs17712224	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1909	0.95[ASN][1000 genomes]
rs1964381	0.92[ASN][1000 genomes]
rs1994414	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1994415	0.95[ASN][1000 genomes]
rs1994416	0.95[ASN][1000 genomes]
rs2016345	0.94[ASN][1000 genomes]
rs2099356	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2163855	0.96[ASN][1000 genomes]
rs2195981	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2217669	0.87[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2356401	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2356403	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2356432	0.96[ASN][1000 genomes]
rs2356433	0.96[ASN][1000 genomes]
rs2356434	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2356438	0.95[ASN][1000 genomes]
rs2356439	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs239948	0.94[ASN][1000 genomes]
rs239949	0.94[ASN][1000 genomes]
rs2883946	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs4511643	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs57096959	0.96[ASN][1000 genomes]
rs57133938	0.95[ASN][1000 genomes]
rs59503823	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60036744	0.95[ASN][1000 genomes]
rs60085895	0.93[ASN][1000 genomes]
rs62114569	0.95[ASN][1000 genomes]
rs62118368	0.95[ASN][1000 genomes]
rs62118369	0.96[ASN][1000 genomes]
rs62118371	0.95[ASN][1000 genomes]
rs62118372	0.95[ASN][1000 genomes]
rs6509120	0.95[ASN][1000 genomes]
rs7247308	0.96[ASN][1000 genomes]
rs7247863	0.95[ASN][1000 genomes]
rs7248807	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7249057	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7249413	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7253002	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7253384	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7253606	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7254659	0.86[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7259647	0.92[ASN][1000 genomes]
rs73052639	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73052665	0.95[ASN][1000 genomes]
rs7508701	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099861	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8106802	0.95[ASN][1000 genomes]
rs8112065	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8113286	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs349032	ZNF296	cis	parietal	SCAN
rs349032	PPP1R13L	cis	cerebellum	SCAN
rs349032	TBC1D17	cis	parietal	SCAN
rs349032	CD3EAP	cis	cerebellum	SCAN
rs349032	ZNF404	trans	parietal	SCAN
rs349032	KCNN4	cis	multi-tissue	Pritchard
rs349032	SYMPK	cis	cerebellum	SCAN
rs349032	LYPD5	cis	brain	seeQTL
rs349032	KLK8	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44313800-44319200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:44314000-44318800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:44314200-44318800	Weak transcription	HMEC	breast
4	chr19:44314200-44318800	Weak transcription	NHEK	skin
5	chr19:44315600-44317800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:44316200-44317400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links