Variant report

Variant	rs17697894
Chromosome Location	chr7:86582891-86582892
allele	C/T
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	chr7:86570162..86571702-chr7:86582796..86584341,2	K562	blood:
3	chr7:86570202..86573182-chr7:86582610..86584341,2	K562	blood:
4	chr7:86581994..86583701-chr7:86822777..86825606,2	K562	blood:

Variant related genes	Relation type
ENSG00000135185	Chromatin interaction
ENSG00000164659	Chromatin interaction
ENSG00000135164	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1014634	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10215436	0.92[AFR][1000 genomes]
rs10232633	0.86[EUR][1000 genomes]
rs10236047	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][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[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10263372	1.00[CEU][hapmap]
rs10267763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs1029367	0.91[AFR][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];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11979332	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]
rs11981220	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12111888	1.00[CEU][hapmap];0.92[AFR][1000 genomes]
rs12113681	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];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[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs17161118	1.00[CEU][hapmap]
rs17697806	0.86[ASN][1000 genomes]
rs17697878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17765493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2788868	1.00[CHB][hapmap]
rs28362761	0.95[AFR][1000 genomes]
rs28405414	0.89[AFR][1000 genomes]
rs28410495	0.91[AFR][1000 genomes]
rs28490267	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28583791	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28635668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35895874	0.89[AFR][1000 genomes]
rs61082072	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6465089	1.00[YRI][hapmap];0.91[AFR][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];0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs73382367	0.88[AFR][1000 genomes]
rs73382375	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73382388	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73382401	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73384105	0.91[EUR][1000 genomes]
rs7781782	1.00[CEU][hapmap];0.86[MKK][hapmap]
rs7783745	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17697894	STEAP4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86577800-86583000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:86578000-86585600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:86579000-86585400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:86579200-86585600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:86579200-86585800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:86579200-86594400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:86579400-86592800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:86579600-86588600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:86580200-86592800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:86580200-86596000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:86580400-86583200	Weak transcription	GM12878-XiMat	blood
12	chr7:86580600-86585600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr7:86582000-86583000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:86582400-86583800	Enhancers	Brain Hippocampus Middle	brain
15	chr7:86582600-86583000	Enhancers	Brain Substantia Nigra	brain
16	chr7:86582600-86583200	Enhancers	Brain Anterior Caudate	brain
17	chr7:86582600-86583400	Enhancers	Brain Angular Gyrus	brain
18	chr7:86582600-86583600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr7:86582600-86583600	Enhancers	HepG2	liver
20	chr7:86582600-86584800	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr7:86582600-86585200	Enhancers	Brain Cingulate Gyrus	brain

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