Variant report

Variant	rs9647948
Chromosome Location	chr7:71503303-71503304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:82275396..82277038-chr7:71501737..71504586,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10216301	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10247062	0.85[ASN][1000 genomes]
rs10250790	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10251795	0.85[ASN][1000 genomes]
rs10267684	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10950300	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11772518	1.00[CHB][hapmap]
rs11981190	1.00[JPT][hapmap]
rs1232514	1.00[JPT][hapmap]
rs12533623	1.00[CHB][hapmap]
rs12699125	1.00[JPT][hapmap]
rs13230379	1.00[JPT][hapmap]
rs1474389	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17605262	1.00[CHB][hapmap]
rs17673882	1.00[JPT][hapmap]
rs17673922	1.00[JPT][hapmap]
rs1859485	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1996399	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2158562	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2189846	1.00[CHB][hapmap]
rs2867566	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2867603	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2867605	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34173611	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34501524	0.85[ASN][1000 genomes]
rs34722735	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577845	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4717627	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4717631	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4719206	0.85[ASN][1000 genomes]
rs548613	1.00[JPT][hapmap]
rs6953054	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6954622	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6979774	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7784022	0.85[ASN][1000 genomes]
rs7786666	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7795273	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7803192	1.00[CHB][hapmap]
rs7805893	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7808523	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs844675	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs844719	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs844729	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844762	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs844767	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs860007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs860010	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs860013	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs860014	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs865225	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs875499	1.00[JPT][hapmap]
rs917211	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[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	nsv1026896	chr7:71003462-71721516	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS 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	6 gene(s)	inside rSNPs	diseases
2	nsv1027496	chr7:71162362-71575116	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916220	chr7:71200006-71708048	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv531372	chr7:71300090-71909517	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv491610	chr7:71422560-71803630	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv831023	chr7:71443549-71588033	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv531373	chr7:71487076-71765613	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv817506	chr7:71488542-71935721	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9647948	GTF2IRD1	cis	cerebellum	SCAN
rs9647948	TBL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71493400-71503600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:71498800-71507000	Weak transcription	Thymus	Thymus
3	chr7:71502000-71504200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr7:71502400-71504400	Enhancers	Dnd41	blood
5	chr7:71502400-71505200	Enhancers	Primary hematopoietic stem cells	blood
6	chr7:71502600-71506400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:71502800-71503600	Genic enhancers	Fetal Thymus	thymus
8	chr7:71503200-71503800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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