Variant report

Variant	rs2613902
Chromosome Location	chr12:74943804-74943805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:74943223..74946956-chr12:74947283..74950877,6	K562	blood:
2	chr12:74936725..74942637-chr12:74943509..74950364,10	MCF-7	breast:
3	chr12:74941646..74944440-chr12:74957364..74960254,2	K562	blood:
4	chr12:74938864..74942058-chr12:74943211..74947418,4	K562	blood:
5	chr12:74930467..74932875-chr12:74943697..74946304,2	MCF-7	breast:
6	chr12:74943282..74945099-chr12:74957128..74958764,2	MCF-7	breast:
7	chr12:74943223..74946956-chr12:74948015..74950877,4	K562	blood:

Variant related genes	Relation type
ENSG00000253719	Chromatin interaction
ENSG00000257386	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12809241	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12825946	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1493796	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1493810	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17113674	0.83[ASN][1000 genomes]
rs17113675	0.83[ASN][1000 genomes]
rs17113679	0.83[ASN][1000 genomes]
rs17113748	0.94[ASN][1000 genomes]
rs17113750	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17180010	1.00[JPT][hapmap]
rs2061579	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2126136	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2365919	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2605375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2605381	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2641470	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2641471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35454023	0.83[ASN][1000 genomes]
rs4547177	0.83[ASN][1000 genomes]
rs4882643	0.90[ASN][1000 genomes]
rs58783285	0.83[ASN][1000 genomes]
rs590352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60905363	0.83[ASN][1000 genomes]
rs67506065	0.98[ASN][1000 genomes]
rs7132047	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs725181	0.94[ASN][1000 genomes]
rs7295970	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7957387	1.00[JPT][hapmap]
rs7962722	0.83[ASN][1000 genomes]
rs7964349	1.00[JPT][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	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv899293	chr12:74835107-74995760	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv899295	chr12:74854750-74984992	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv470303	chr12:74880668-74945356	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	n/a
5	nsv899296	chr12:74880668-74974630	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2613902	ATXN7L3B	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74935200-74945000	Weak transcription	Left Ventricle	heart
2	chr12:74936000-74945600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:74936400-74945000	Weak transcription	Fetal Heart	heart
4	chr12:74937600-74944400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:74937600-74944600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:74943600-74945200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links