Variant report

Variant	rs9653257
Chromosome Location	chr2:213078248-213078249
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10048673	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs10048750	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs10048796	0.82[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs10048819	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs10164682	0.82[CEU][hapmap]
rs10166172	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10172782	0.83[CHB][hapmap]
rs10184205	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs10190345	0.86[CHB][hapmap]
rs10196229	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10201835	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10206443	0.82[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap]
rs10207020	0.86[CHD][hapmap]
rs10804203	0.86[CHB][hapmap]
rs10932424	0.86[CHB][hapmap]
rs10932426	0.83[CHB][hapmap]
rs10932427	0.84[CHB][hapmap]
rs10932428	0.93[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs11677623	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs11682936	0.86[CHB][hapmap]
rs11693640	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs11887771	0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11896691	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs12052282	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs12185587	0.84[CHB][hapmap]
rs12468821	0.86[CHB][hapmap]
rs12622947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13391312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13407289	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs13408933	0.86[CHB][hapmap]
rs13416059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13427258	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13429136	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs13432680	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1357136	0.88[CEU][hapmap];0.80[CHB][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs1357137	0.94[EUR][1000 genomes]
rs1357138	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs1357139	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs1402764	0.86[CHB][hapmap]
rs1402769	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap]
rs1467273	0.86[CHB][hapmap]
rs1467275	0.86[CHB][hapmap]
rs1474258	0.86[CHB][hapmap]
rs1521638	0.83[CEU][hapmap];0.93[EUR][1000 genomes]
rs1521639	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs1521641	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1521642	0.96[EUR][1000 genomes]
rs1521646	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1521649	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs1521659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1546718	0.86[CHB][hapmap]
rs1546719	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs1915743	0.86[CHB][hapmap]
rs1915747	0.83[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes]
rs1948875	0.83[CHD][hapmap]
rs1949652	0.80[CHB][hapmap]
rs1949654	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs1976839	0.94[EUR][1000 genomes]
rs2049180	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.92[YRI][hapmap]
rs2090862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2103001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4145960	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs4145961	0.86[CHB][hapmap]
rs4233985	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4350692	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs4375810	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs4580336	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs4638732	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs6718075	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6724508	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6755027	0.86[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs7581884	0.86[CHB][hapmap]
rs7592673	0.95[EUR][1000 genomes]
rs7608095	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs9288446	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap]
rs9288447	0.83[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs9288449	0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap]
rs939224	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.80[MEX][hapmap]
rs939226	0.91[CEU][hapmap];0.84[CHB][hapmap]
rs9973372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs9973520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs9973523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011572	chr2:212840066-213152279	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv875805	chr2:212891401-213164837	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875806	chr2:212997024-213211067	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1001718	chr2:213047033-213155985	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1004823	chr2:213052804-213181263	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv536138	chr2:213052804-213181263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1006051	chr2:213052804-213273642	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv875807	chr2:213054058-213103721	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv584346	chr2:213067749-213258622	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv2763085	chr2:213073428-213107281	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9653257	CPS1IT1	cis	parietal	SCAN
rs9653257	PRPSAP2	trans	parietal	SCAN
rs9653257	BARD1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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