Variant report

Variant	rs12538296
Chromosome Location	chr7:140686639-140686640
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	chr7:140686234..140687769-chr7:140687897..140689543,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10215245	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10240888	0.84[ASN][1000 genomes]
rs10243698	0.87[AFR][1000 genomes]
rs10255167	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10265001	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10268118	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1044927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10952364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13234490	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs13236223	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13236704	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs1476816	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs1533933	0.86[EUR][1000 genomes]
rs16882367	0.82[ASN][1000 genomes]
rs1860720	0.83[EUR][1000 genomes]
rs2079827	0.93[ASN][1000 genomes]
rs2079978	0.81[EUR][1000 genomes]
rs246739	0.93[ASN][1000 genomes]
rs3805116	0.85[CHB][hapmap]
rs3852286	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3864527	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38715	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs38717	0.95[ASN][1000 genomes]
rs38718	0.93[ASN][1000 genomes]
rs38720	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs38722	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs38723	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs38726	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs38730	0.84[ASN][1000 genomes]
rs38731	0.84[ASN][1000 genomes]
rs38734	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs38736	0.82[ASN][1000 genomes]
rs38739	1.00[CHB][hapmap]
rs38740	1.00[CHB][hapmap]
rs4726225	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs488795	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs512509	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs528957	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs557962	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs58901822	0.93[ASN][1000 genomes]
rs62485452	0.89[ASN][1000 genomes]
rs62485453	0.93[ASN][1000 genomes]
rs6464217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6464260	0.90[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs6662	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6967214	0.84[EUR][1000 genomes]
rs6971577	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7792447	0.83[EUR][1000 genomes]
rs7801518	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs801127	1.00[CHB][hapmap]
rs9274	1.00[CHB][hapmap]
rs9800952	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1026448	chr7:140636599-140716829	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12538296	TMEM178B	cis	Esophagus Mucosa	GTEx
rs12538296	MRPS33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140686400-140688000	Weak transcription	HepG2	liver
2	chr7:140686600-140686800	Enhancers	Fetal Intestine Large	intestine

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