Variant report

Variant	rs9296487
Chromosome Location	chr6:12849031-12849032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10434854	0.85[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs13192344	0.97[ASN][1000 genomes]
rs13192509	0.97[ASN][1000 genomes]
rs1332840	0.88[CEU][hapmap]
rs1412740	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs1412742	0.97[ASN][1000 genomes]
rs1412743	0.97[ASN][1000 genomes]
rs1412749	0.81[EUR][1000 genomes]
rs1412751	0.88[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1537334	0.85[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1537335	0.97[ASN][1000 genomes]
rs1537336	0.97[ASN][1000 genomes]
rs1537337	0.97[ASN][1000 genomes]
rs1537338	0.85[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1571996	0.85[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs1571997	0.85[CHB][hapmap]
rs1572000	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1572002	0.89[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs16873431	0.85[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs16873436	0.97[ASN][1000 genomes]
rs16873447	0.97[ASN][1000 genomes]
rs16873449	0.97[ASN][1000 genomes]
rs17617207	0.89[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2015764	0.82[EUR][1000 genomes]
rs2026457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2065490	0.97[ASN][1000 genomes]
rs2065491	0.85[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs2184027	0.97[ASN][1000 genomes]
rs35278288	0.85[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs35657920	0.89[ASN][1000 genomes]
rs3945322	0.85[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4142300	0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs4711842	0.85[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4711845	0.97[ASN][1000 genomes]
rs4711848	0.85[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs4714866	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4714868	0.82[EUR][1000 genomes]
rs4714913	0.97[ASN][1000 genomes]
rs4714930	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4714931	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs5017386	0.85[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs56408440	0.94[ASN][1000 genomes]
rs57387500	0.94[ASN][1000 genomes]
rs58666803	0.94[ASN][1000 genomes]
rs60954427	0.90[ASN][1000 genomes]
rs6458460	0.82[EUR][1000 genomes]
rs6458461	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6458493	0.85[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs6458494	0.97[ASN][1000 genomes]
rs6915402	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6915585	0.85[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs6916397	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs6916418	0.81[EUR][1000 genomes]
rs6916421	0.81[EUR][1000 genomes]
rs6917097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6919327	0.83[EUR][1000 genomes]
rs6922969	0.81[EUR][1000 genomes]
rs6924150	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs6938417	0.88[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6941422	0.89[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7454135	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7757205	0.80[EUR][1000 genomes]
rs7757858	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7762547	0.82[EUR][1000 genomes]
rs7764490	0.84[EUR][1000 genomes]
rs7768030	0.85[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7776079	0.89[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs9296465	0.81[EUR][1000 genomes]
rs9296486	0.85[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs9296488	0.85[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs9296494	0.81[TSI][hapmap]
rs9296495	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349344	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9349346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9349350	0.85[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs9349352	0.97[ASN][1000 genomes]
rs9357503	0.85[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs9367239	0.85[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs9367240	0.97[ASN][1000 genomes]
rs9369605	0.97[ASN][1000 genomes]
rs9369607	0.97[ASN][1000 genomes]
rs9369612	0.85[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs9381391	0.81[EUR][1000 genomes]
rs9381427	0.84[ASN][1000 genomes]
rs9381435	0.85[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs9381436	0.97[ASN][1000 genomes]
rs9381439	0.85[CHB][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs9381451	0.85[CHB][hapmap];0.96[CHD][hapmap];0.89[ASN][1000 genomes]
rs9395161	0.85[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs9395162	0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs9395172	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9395185	0.85[CHB][hapmap];0.96[CHD][hapmap];0.89[ASN][1000 genomes]
rs944766	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9463106	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs9463110	0.88[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs9472551	0.89[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs9472672	0.85[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs9472752	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9472790	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830587	chr6:12769661-12939875	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12838600-12849400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:12841000-12849200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:12845200-12849600	Weak transcription	HSMM	muscle
4	chr6:12845600-12851000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:12846000-12849400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:12846200-12849200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:12846400-12851000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:12846800-12849200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:12846800-12849200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:12847200-12849200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:12848800-12849800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:12848800-12849800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:12848800-12850000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:12848800-12851800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr6:12848800-12852000	Enhancers	HUES64 Cell Line	embryonic stem cell

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