Variant report

Variant	rs9646916
Chromosome Location	chr2:125403998-125403999
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10165603	0.88[CEU][hapmap];0.84[CHB][hapmap]
rs10184472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194805	0.85[CEU][hapmap]
rs10195187	0.85[CEU][hapmap]
rs10195554	0.89[EUR][1000 genomes]
rs10196022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10202655	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10202736	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs10206545	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10207721	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11123053	0.85[CEU][hapmap]
rs11123056	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11674701	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs11675141	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11676952	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11686268	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12466900	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs12470814	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12473998	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12990799	0.83[GIH][hapmap]
rs12995183	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13003103	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13011609	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1394141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1394142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1394143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1394146	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1454133	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs1504015	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1504023	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1587788	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1587789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1604806	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1902004	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs1910528	0.85[CEU][hapmap]
rs2047874	0.85[CEU][hapmap];0.93[GIH][hapmap]
rs2219107	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4848249	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs4848250	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs4848251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4848252	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4848257	0.90[ASN][1000 genomes]
rs4848947	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4848949	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4848950	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs4848953	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4848956	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4848957	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4848959	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4848960	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6541962	0.85[CEU][hapmap]
rs6541966	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs6707181	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6707400	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6707412	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6712020	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6720324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6721614	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6727845	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6739364	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6743015	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6745271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750530	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6751507	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6754751	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs727179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs727180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7558706	0.85[CEU][hapmap]
rs7560341	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584599	0.85[CEU][hapmap]
rs7586683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7599608	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7599787	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7605511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs924802	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs924803	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs936028	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs936029	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs963189	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs963190	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs9646915	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv834357	chr2:125258157-125421507	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv834359	chr2:125367872-125536022	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
3	nsv428727	chr2:125372897-125512949	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:125403600-125404200	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr2:125403800-125404600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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