Variant report

Variant	rs550675
Chromosome Location	chr6:70979193-70979194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1135056	0.94[JPT][hapmap];0.94[MEX][hapmap];0.87[ASN][1000 genomes]
rs113979	0.96[CEU][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1200579	0.85[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap]
rs1200580	0.85[CEU][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap]
rs12191701	0.80[GIH][hapmap]
rs1753208	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2024730	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2076816	0.80[YRI][hapmap]
rs2274586	0.84[ASN][1000 genomes]
rs500457	0.96[CEU][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs507676	0.94[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs519068	0.82[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs528080	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs535308	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs544179	0.81[CEU][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap]
rs546628	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs555663	0.89[MEX][hapmap]
rs590656	0.84[MEX][hapmap]
rs604896	0.82[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs701686	0.96[CEU][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs701688	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs701689	0.94[JPT][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs701690	0.86[ASN][1000 genomes]
rs701693	0.94[ASW][hapmap];0.92[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv886143	chr6:70968276-70984436	Strong transcription Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70952200-70980400	Weak transcription	Fetal Stomach	stomach
2	chr6:70952200-70990000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:70952600-70980400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:70952800-70989800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:70962000-70983600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:70965200-70991600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:70979000-70991600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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