Variant report

Variant	rs9309970
Chromosome Location	chr3:85171302-85171303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10433523	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11127873	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11127876	0.86[CHB][hapmap]
rs11127877	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11127880	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11127882	0.85[CHB][hapmap]
rs11127883	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs11127884	0.82[CHB][hapmap]
rs11713170	0.81[EUR][1000 genomes]
rs12053927	0.85[CHB][hapmap]
rs12486784	0.82[CHB][hapmap]
rs12486846	0.85[CHB][hapmap]
rs12487792	0.86[YRI][hapmap]
rs12488308	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs13059287	0.96[ASN][1000 genomes]
rs13061527	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs13064817	0.85[EUR][1000 genomes]
rs13097560	0.85[CHB][hapmap]
rs13101042	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1349602	0.85[CHB][hapmap]
rs1376936	0.85[CHB][hapmap];0.87[YRI][hapmap]
rs1376938	0.85[CHB][hapmap]
rs1452122	0.82[CHB][hapmap]
rs1452123	0.82[CHB][hapmap]
rs1452126	0.85[CHB][hapmap]
rs1452127	0.82[CHB][hapmap]
rs1545926	1.00[CHB][hapmap]
rs1968691	0.85[CHB][hapmap]
rs1994315	0.81[EUR][1000 genomes]
rs2034619	0.82[CHB][hapmap]
rs2167606	0.82[CHB][hapmap]
rs2171140	0.80[AMR][1000 genomes]
rs2171141	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2200464	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2220243	0.80[EUR][1000 genomes]
rs2220244	1.00[CHB][hapmap]
rs2290339	0.85[CHB][hapmap]
rs2326128	0.89[EUR][1000 genomes]
rs4410457	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62250629	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6549011	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6549012	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6765011	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6775464	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775752	0.85[CHB][hapmap]
rs6775792	0.85[CHB][hapmap];0.80[YRI][hapmap]
rs6780644	0.82[CHB][hapmap]
rs6788656	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789415	0.85[CHB][hapmap]
rs6790864	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6796256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796393	0.96[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6798922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6799730	0.85[CHB][hapmap]
rs7623714	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7630177	0.85[CHB][hapmap];0.83[YRI][hapmap]
rs7632628	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs7632909	1.00[ASN][1000 genomes]
rs7635613	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs7636138	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7637886	0.81[YRI][hapmap]
rs7645049	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7646739	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7647649	0.82[EUR][1000 genomes]
rs9309969	0.80[EUR][1000 genomes]
rs9681960	0.85[CHB][hapmap]
rs9810830	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs9813787	0.85[CHB][hapmap]
rs9814600	0.83[EUR][1000 genomes]
rs9814835	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9818067	0.82[CHB][hapmap]
rs9819278	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs9820587	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9866167	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs9875381	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs9882148	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs9882296	0.85[CHB][hapmap];0.84[YRI][hapmap]
rs9883252	1.00[CHB][hapmap]
rs994237	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv492289	chr3:85066623-85319147	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv877093	chr3:85101501-85194054	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590897	chr3:85122624-85187085	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv877094	chr3:85124697-85253981	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv590898	chr3:85158733-85243777	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv877095	chr3:85163167-85290434	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv877096	chr3:85163167-85366517	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv460747	chr3:85163167-85391672	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv590899	chr3:85163167-85391672	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1001124	chr3:85167047-85309046	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85168400-85177600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85169200-85198600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:85170800-85171800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:85170800-85173000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:85171200-85171600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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