Variant report

Variant	rs13214717
Chromosome Location	chr6:109894354-109894355
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1048203	0.81[CEU][hapmap]
rs10499052	0.94[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10499053	0.85[CEU][hapmap]
rs10782162	0.85[CEU][hapmap];1.00[LWK][hapmap]
rs11753645	0.94[CEU][hapmap]
rs11964533	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs12197114	0.81[CEU][hapmap]
rs12208933	0.85[CEU][hapmap];0.81[AFR][1000 genomes]
rs12524639	0.81[CEU][hapmap]
rs12529505	0.94[CEU][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap]
rs12661287	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13191444	0.87[YRI][hapmap]
rs13195462	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13195517	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs13199519	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs13203636	0.93[CEU][hapmap]
rs13204787	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13207864	0.83[AMR][1000 genomes]
rs13211604	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs13212535	0.80[AMR][1000 genomes]
rs1321328	0.85[CEU][hapmap]
rs13215994	0.83[AMR][1000 genomes]
rs1358998	0.81[CEU][hapmap]
rs1923725	0.81[CEU][hapmap]
rs28823411	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3757234	0.81[CEU][hapmap]
rs6914498	0.84[CEU][hapmap]
rs7773095	0.81[CEU][hapmap]
rs9480948	0.81[CEU][hapmap]
rs9480957	0.81[CEU][hapmap]
rs9487100	0.80[CEU][hapmap]
rs971434	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	nsv1026012	chr6:109851638-109999379	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv604484	chr6:109851937-109997529	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1019389	chr6:109868058-109987502	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538416	chr6:109868058-109987502	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv917318	chr6:109885195-109982375	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13214717	SMPD2	cis	Whole Blood	GTEx
rs13214717	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs13214717	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs13214717	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs13214717	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109878800-109903600	Weak transcription	Psoas Muscle	Psoas
2	chr6:109879000-109903800	Weak transcription	Thymus	Thymus
3	chr6:109879000-109906000	Weak transcription	Left Ventricle	heart
4	chr6:109879000-109917400	Weak transcription	Aorta	Aorta
5	chr6:109879800-109900600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:109880800-109900000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:109881000-109900000	Weak transcription	Adipose Nuclei	Adipose
8	chr6:109881200-109902400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:109885000-109902400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:109885200-109900200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:109886000-109910600	Weak transcription	Primary B cells from cord blood	blood
12	chr6:109893400-109894800	Strong transcription	Primary T cells from cord blood	blood
13	chr6:109894000-109894800	Strong transcription	Pancreas	Pancrea

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