Variant report

Variant	rs1557665
Chromosome Location	chr7:86577346-86577347
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr7:86577199-86577717	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr7:86577227-86577588	Hela-S3	cervix:	n/a	n/a
3	CHD2	chr7:86577254-86577634	Hela-S3	cervix:	n/a	n/a
4	TEAD4	chr7:86577253-86577657	HepG2	liver:	n/a	n/a
5	BRCA1	chr7:86577244-86577596	Hela-S3	cervix:	n/a	n/a
6	ZKSCAN1	chr7:86577252-86577801	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr7:86577227-86577665	H1-hESC	embryonic stem cell:	n/a	chr7:86577382-86577393
8	CEBPB	chr7:86577322-86577517	K562	blood:	n/a	chr7:86577382-86577393
9	RFX5	chr7:86577122-86577646	Hela-S3	cervix:	n/a	n/a
10	RCOR1	chr7:86576975-86577666	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr7:86577274-86577525	A549	lung:	n/a	chr7:86577382-86577393
12	USF2	chr7:86577063-86577738	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr7:86576967-86577783	Hela-S3	cervix:	n/a	chr7:86577382-86577393
14	MAX	chr7:86577277-86577610	Hela-S3	cervix:	n/a	n/a
15	CEBPB	chr7:86577225-86577570	HepG2	liver:	n/a	chr7:86577382-86577393
16	EP300	chr7:86577210-86577620	Hela-S3	cervix:	n/a	chr7:86577362-86577371
17	STAT3	chr7:86577213-86577593	Hela-S3	cervix:	n/a	chr7:86577361-86577369
18	TCF7L2	chr7:86577108-86577679	Hela-S3	cervix:	n/a	n/a
19	TEAD4	chr7:86577238-86577622	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:86567674..86570136-chr7:86576947..86578810,2	K562	blood:
2	chr7:86571340..86575595-chr7:86576570..86580636,6	K562	blood:

Variant related genes	Relation type
KIAA1324L	TF binding region
ENSG00000164659	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1014634	1.00[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];0.94[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];0.94[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10271867	0.88[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs11974622	1.00[CEU][hapmap];0.94[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]
rs11979332	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]
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]
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];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]
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];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2373361	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.89[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];0.94[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];0.94[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
rs1557665	STEAP4	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86539200-86578800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr7:86561800-86578600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:86563000-86578200	Weak transcription	HUVEC	blood vessel
4	chr7:86567600-86578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:86569200-86581400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:86569400-86578600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:86572200-86578400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:86572600-86578800	Weak transcription	Brain Anterior Caudate	brain
9	chr7:86573000-86577400	Weak transcription	K562	blood
10	chr7:86573600-86577600	Weak transcription	Brain Angular Gyrus	brain
11	chr7:86573600-86582600	Weak transcription	Gastric	stomach
12	chr7:86574600-86578000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:86576000-86579000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr7:86576200-86577400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr7:86576200-86577600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr7:86576200-86578000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr7:86576200-86580200	Enhancers	Brain Hippocampus Middle	brain
18	chr7:86576200-86580400	Enhancers	Brain Substantia Nigra	brain
19	chr7:86576400-86577400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr7:86576400-86577800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:86576400-86578000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr7:86576400-86578000	Enhancers	Hela-S3	cervix
23	chr7:86576400-86579200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr7:86576400-86579800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:86576800-86577800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr7:86576800-86581200	Weak transcription	Fetal Stomach	stomach
27	chr7:86577000-86577600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr7:86577000-86577600	Enhancers	Aorta	Aorta
29	chr7:86577000-86577600	Enhancers	Right Atrium	heart
30	chr7:86577000-86577800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr7:86577000-86577800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr7:86577000-86577800	Enhancers	Fetal Heart	heart
33	chr7:86577000-86579000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:86577200-86577600	Enhancers	Adipose Nuclei	Adipose
35	chr7:86577200-86577800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr7:86577200-86578800	Weak transcription	Pancreas	Pancrea
37	chr7:86577200-86579000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr7:86577200-86579400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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