Variant report

Variant	rs6712119
Chromosome Location	chr2:50409327-50409328
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10490233	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10490240	0.81[CEU][hapmap]
rs11125290	0.92[CEU][hapmap]
rs11125291	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs11125292	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs11125294	0.93[CEU][hapmap];0.83[AMR][1000 genomes]
rs11125295	0.93[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs11125296	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11888330	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs11896556	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11900502	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12466807	0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12468151	0.81[AMR][1000 genomes]
rs12468252	0.93[CEU][hapmap];0.81[AMR][1000 genomes]
rs12468282	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12468396	0.81[AMR][1000 genomes]
rs12468477	0.93[CEU][hapmap];0.81[TSI][hapmap]
rs12470518	0.80[CHB][hapmap]
rs12475100	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12476530	0.80[CHB][hapmap]
rs12478603	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs12613266	0.80[AMR][1000 genomes]
rs12613363	0.85[CHB][hapmap]
rs12622844	0.93[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes]
rs1377238	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs1402166	0.88[CHD][hapmap]
rs1421573	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs1452769	0.92[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1452770	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1452771	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1517827	0.82[MEX][hapmap]
rs1563019	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs1563028	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs1584763	0.93[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs17039764	0.85[CHB][hapmap]
rs17039905	0.80[AMR][1000 genomes]
rs17039932	0.93[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs17039940	0.93[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes]
rs17039947	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs17039976	0.93[CEU][hapmap]
rs17039979	0.93[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs17039985	0.93[CEU][hapmap];0.80[AMR][1000 genomes]
rs17040013	0.93[CEU][hapmap]
rs17040034	0.93[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs17040064	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs17040090	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17040117	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs17040123	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17040138	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17040141	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17040147	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17040160	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17040169	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17040207	0.86[JPT][hapmap]
rs17040210	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs17040235	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs1915225	0.81[CHB][hapmap]
rs1915227	0.90[CHD][hapmap]
rs2176872	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2218979	0.85[CHB][hapmap]
rs4971649	0.91[CEU][hapmap];0.80[AMR][1000 genomes]
rs4971650	0.93[CEU][hapmap]
rs4971652	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971653	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971654	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971655	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4971656	0.93[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs4971658	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971659	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4971661	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60500567	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545149	0.85[CHB][hapmap]
rs6545155	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6712102	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6712423	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6731397	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs72878157	0.80[AMR][1000 genomes]
rs7599349	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7607863	0.93[CEU][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	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv934303	chr2:50145598-50412189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2756107	chr2:50307245-50440043	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948833	chr2:50307245-50459077	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1002344	chr2:50326207-50518933	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv535692	chr2:50326207-50518933	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6712119	CRIPT	cis	cerebellum	SCAN
rs6712119	ATP6V1E2	cis	parietal	SCAN

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

No data

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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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