Variant report

Variant	rs12042770
Chromosome Location	chr1:190419635-190419636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10429905	0.81[CEU][hapmap]
rs10800941	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10920705	0.81[CEU][hapmap]
rs10920715	0.81[CEU][hapmap]
rs10920716	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10920719	0.86[ASN][1000 genomes]
rs10920720	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10920722	0.85[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10920724	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10920725	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10920726	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11577277	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12025018	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12040733	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12043892	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12058472	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078918	0.83[ASN][1000 genomes]
rs12087474	0.81[JPT][hapmap]
rs12089382	1.00[ASN][1000 genomes]
rs12091129	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12093056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12095592	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12097042	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12732361	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12732902	0.81[CEU][hapmap]
rs1442568	0.81[CEU][hapmap]
rs16832345	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16832366	0.86[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2047704	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34302050	0.88[ASN][1000 genomes]
rs3931875	0.81[CEU][hapmap]
rs6658194	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6660355	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6664710	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72731179	0.85[ASN][1000 genomes]
rs7547903	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs872177	0.81[JPT][hapmap]
rs980043	0.86[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932040	chr1:190005334-190914580	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv872758	chr1:190351677-190510003	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv872759	chr1:190371671-190446098	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv872760	chr1:190377988-190577336	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv872761	chr1:190389741-190485034	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv872762	chr1:190389741-190510003	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv872763	chr1:190389741-190531642	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv872764	chr1:190399946-190531642	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv872765	chr1:190418653-190464647	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:190379400-190420000	Weak transcription	Fetal Intestine Large	intestine
2	chr1:190411000-190425600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:190419200-190420800	Enhancers	Duodenum Mucosa	Duodenum
4	chr1:190419400-190419800	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links