Variant report

Variant	rs1997628
Chromosome Location	chr11:9124681-9124682
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9104308..9107322-chr11:9124502..9128223,3	MCF-7	breast:
2	chr11:9123650..9128342-chr11:9129047..9134546,16	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10047438	0.90[ASN][1000 genomes]
rs1039210	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10769991	0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769992	0.83[JPT][hapmap]
rs10769993	0.86[CEU][hapmap]
rs10769995	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10769996	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10840174	0.94[EUR][1000 genomes]
rs10840176	0.91[ASN][1000 genomes]
rs10840178	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840179	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840181	0.83[ASN][1000 genomes]
rs10840182	0.83[ASN][1000 genomes]
rs10840183	0.90[ASN][1000 genomes]
rs10840185	0.84[ASN][1000 genomes]
rs11042195	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042199	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs11604616	0.95[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17256375	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs1874822	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2133217	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2291839	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs2647537	0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2742467	0.88[EUR][1000 genomes]
rs2742556	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2742557	0.89[ASN][1000 genomes]
rs3898554	0.95[CEU][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4910035	0.83[ASN][1000 genomes]
rs56077948	0.83[ASN][1000 genomes]
rs56216908	0.84[ASN][1000 genomes]
rs7109745	0.87[ASN][1000 genomes]
rs7123970	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs7128469	0.82[ASN][1000 genomes]
rs7394878	0.88[CHB][hapmap]
rs7395347	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7395846	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7925308	0.88[CHB][hapmap]
rs7930507	0.88[CHB][hapmap]
rs7947251	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7948219	0.88[EUR][1000 genomes]
rs9888257	0.92[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv467704	chr11:9059192-9125301	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv553454	chr11:9059192-9125301	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1997628	OR10A6	cis	cerebellum	SCAN
rs1997628	OR56A1	cis	cerebellum	SCAN
rs1997628	RASSF10	cis	cerebellum	SCAN
rs1997628	TMEM41B	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9113600-9159800	Weak transcription	Right Ventricle	heart
2	chr11:9114200-9136200	Weak transcription	Fetal Heart	heart
3	chr11:9115000-9141800	Weak transcription	HSMM	muscle
4	chr11:9115200-9134400	Weak transcription	Fetal Stomach	stomach
5	chr11:9119000-9124800	Weak transcription	Pancreas	Pancrea
6	chr11:9121800-9154800	Weak transcription	Brain Substantia Nigra	brain
7	chr11:9124000-9126000	Weak transcription	Gastric	stomach
8	chr11:9124600-9125000	Bivalent Enhancer	HepG2	liver

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