Variant report

Variant	rs7031088
Chromosome Location	chr9:97253578-97253579
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97242816..97244907-chr9:97253508..97257110,3	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1752786	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2006685	0.84[ASN][1000 genomes]
rs2049008	0.93[ASN][1000 genomes]
rs2277182	0.90[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2479602	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2769119	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs3131910	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs4434674	0.83[ASN][1000 genomes]
rs4477096	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4497033	0.84[ASN][1000 genomes]
rs4509403	0.92[ASN][1000 genomes]
rs4743953	0.95[ASN][1000 genomes]
rs4743954	0.96[ASN][1000 genomes]
rs4743955	0.92[ASN][1000 genomes]
rs4744340	0.82[ASN][1000 genomes]
rs4744346	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6479537	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs684892	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs688165	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7020879	0.93[ASN][1000 genomes]
rs7023744	0.83[ASN][1000 genomes]
rs7023915	0.83[ASN][1000 genomes]
rs7024159	0.92[ASN][1000 genomes]
rs7025755	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7027465	0.94[ASN][1000 genomes]
rs7027489	0.90[ASN][1000 genomes]
rs7031496	0.96[ASN][1000 genomes]
rs7031949	0.99[ASN][1000 genomes]
rs7037190	0.99[ASN][1000 genomes]
rs7037198	0.93[ASN][1000 genomes]
rs7038593	0.81[ASN][1000 genomes]
rs7040577	0.83[ASN][1000 genomes]
rs7040710	0.94[ASN][1000 genomes]
rs7041503	0.85[ASN][1000 genomes]
rs7047279	0.93[ASN][1000 genomes]
rs7047295	0.97[ASN][1000 genomes]
rs7047930	0.96[ASN][1000 genomes]
rs7048688	0.99[ASN][1000 genomes]
rs7848221	0.84[ASN][1000 genomes]
rs7848227	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs7853182	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7860616	0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs7863310	0.84[ASN][1000 genomes]
rs7863312	0.84[ASN][1000 genomes]
rs7868562	0.98[ASN][1000 genomes]
rs7873525	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9299421	0.90[ASN][1000 genomes]
rs9299422	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9409511	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs9409512	0.86[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs9409513	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs9409552	0.84[ASN][1000 genomes]
rs9409759	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9409763	0.83[ASN][1000 genomes]
rs9409765	0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9409777	0.93[ASN][1000 genomes]
rs9409779	0.93[ASN][1000 genomes]
rs9409792	0.89[ASN][1000 genomes]
rs9409793	0.80[ASN][1000 genomes]
rs9777207	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
2	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
3	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv893594	chr9:97221463-97283226	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv972423	chr9:97243765-97254596	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv614916	chr9:97245822-97273659	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv969694	chr9:97250110-97254596	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7031088	HIATL1	cis	parietal	SCAN
rs7031088	CDC14B	cis	parietal	SCAN
rs7031088	HIATL1	cis	lung	GTEx
rs7031088	RP11-307E17.8	cis	Esophagus Muscularis	GTEx
rs7031088	HIATL1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97241800-97262800	Weak transcription	Liver	Liver

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