Variant report

Variant	rs11979332
Chromosome Location	chr7:86581745-86581746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:86581703..86583282-chr7:86848670..86850285,2	MCF-7	breast:
2	chr7:86578487..86581845-chr7:86586370..86588762,3	K562	blood:
3	chr19:13261771..13264405-chr7:86579886..86582826,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160888	Chromatin interaction
ENSG00000135185	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1014634	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10232633	0.86[EUR][1000 genomes]
rs10236047	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs10236910	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs10257473	0.94[EUR][1000 genomes]
rs10258008	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs10263372	1.00[CEU][hapmap]
rs10267763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10271867	0.88[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs11974622	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs11976876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11981220	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12111888	1.00[CEU][hapmap]
rs12113681	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1476455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1557665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161067	1.00[CEU][hapmap]
rs17161070	0.88[EUR][1000 genomes]
rs17161096	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs17161098	1.00[CEU][hapmap]
rs17161118	1.00[CEU][hapmap]
rs17697806	0.86[ASN][1000 genomes]
rs17697878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17697894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17765493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2299231	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2373361	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2788868	1.00[CHB][hapmap]
rs28490267	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28583791	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28635668	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61082072	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6965029	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6972489	1.00[CEU][hapmap]
rs73382375	0.94[EUR][1000 genomes]
rs73382388	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73382401	0.91[EUR][1000 genomes]
rs73384105	0.91[EUR][1000 genomes]
rs7781782	1.00[CEU][hapmap]
rs7783745	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7808623	1.00[CEU][hapmap]
rs7810135	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9640574	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025032	chr7:86032479-86642973	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv1015870	chr7:86490491-86802320	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
6	nsv539000	chr7:86490491-86802320	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
7	nsv527889	chr7:86496042-86832603	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11979332	STEAP4	cis	cerebellum	SCAN
rs11979332	BIRC3	trans	brain	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86573600-86582600	Weak transcription	Gastric	stomach
2	chr7:86577800-86582600	Weak transcription	HepG2	liver
3	chr7:86577800-86583000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:86578000-86585600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:86579000-86585400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:86579200-86582200	Weak transcription	Pancreas	Pancrea
7	chr7:86579200-86585600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:86579200-86585800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr7:86579200-86594400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:86579400-86592800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:86579600-86588600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:86580000-86582600	Weak transcription	Brain Anterior Caudate	brain
13	chr7:86580200-86582400	Weak transcription	Brain Hippocampus Middle	brain
14	chr7:86580200-86582600	Weak transcription	Brain Angular Gyrus	brain
15	chr7:86580200-86582600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:86580200-86592800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:86580200-86596000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:86580400-86582600	Weak transcription	Brain Substantia Nigra	brain
19	chr7:86580400-86583200	Weak transcription	GM12878-XiMat	blood
20	chr7:86580600-86585600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:86580800-86582000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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