Variant report

Variant	rs4693788
Chromosome Location	chr4:87770462-87770463
allele	A/G
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	POLR2A	chr4:87770325-87770809	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr4:87770307-87770729	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr4:87770458-87770738	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr4:87770292-87770734	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr4:87770292-87770798	MCF10A-Er-Src	breast:	n/a	chr4:87770753-87770760
6	EP300	chr4:87770389-87770677	Hela-S3	cervix:	n/a	n/a
7	FOS	chr4:87770349-87770722	MCF10A-Er-Src	breast:	n/a	chr4:87770516-87770524
8	MYC	chr4:87770408-87770628	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr4:87770272-87770798	MCF10A-Er-Src	breast:	n/a	chr4:87770753-87770760
10	STAT3	chr4:87770268-87770805	MCF10A-Er-Src	breast:	n/a	chr4:87770753-87770760
11	SMC3	chr4:87770461-87770732	Hela-S3	cervix:	n/a	n/a
12	FOS	chr4:87770244-87770736	MCF10A-Er-Src	breast:	n/a	chr4:87770516-87770524
13	POLR2A	chr4:87770292-87770834	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr4:87770356-87770656	MCF10A-Er-Src	breast:	n/a	chr4:87770516-87770524
15	FOS	chr4:87770246-87770733	MCF10A-Er-Src	breast:	n/a	chr4:87770516-87770524

Variant related genes	Relation type
SLC10A6	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10017360	0.86[ASN][1000 genomes]
rs10029698	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs11731586	0.86[ASN][1000 genomes]
rs11935015	0.86[ASN][1000 genomes]
rs11939730	0.86[ASN][1000 genomes]
rs12186239	0.85[EUR][1000 genomes]
rs12503661	0.86[ASN][1000 genomes]
rs13103212	0.88[EUR][1000 genomes]
rs13117826	0.88[EUR][1000 genomes]
rs13131035	0.85[EUR][1000 genomes]
rs13134746	0.88[EUR][1000 genomes]
rs13137142	0.98[ASN][1000 genomes]
rs13141097	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13147739	0.85[CEU][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs13147942	0.88[EUR][1000 genomes]
rs13151671	0.82[EUR][1000 genomes]
rs13151797	0.81[EUR][1000 genomes]
rs1374934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1550931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2594281	0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2594282	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2594284	0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2705622	0.86[ASN][1000 genomes]
rs2705623	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2705624	0.91[ASN][1000 genomes]
rs2705626	0.81[ASN][1000 genomes]
rs2705627	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28407685	0.82[EUR][1000 genomes]
rs28439108	0.88[EUR][1000 genomes]
rs28447475	0.88[EUR][1000 genomes]
rs28502831	0.85[EUR][1000 genomes]
rs28610346	0.82[EUR][1000 genomes]
rs28629974	0.85[EUR][1000 genomes]
rs28661703	0.83[EUR][1000 genomes]
rs28664715	0.85[EUR][1000 genomes]
rs28729679	0.88[EUR][1000 genomes]
rs28854225	0.85[EUR][1000 genomes]
rs28886889	0.85[EUR][1000 genomes]
rs2922234	0.88[ASN][1000 genomes]
rs4508849	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4693789	0.86[ASN][1000 genomes]
rs56414102	0.82[ASN][1000 genomes]
rs57477100	0.98[ASN][1000 genomes]
rs58275023	0.88[ASN][1000 genomes]
rs6531936	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.98[ASN][1000 genomes]
rs6531937	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.98[ASN][1000 genomes]
rs71605624	0.85[EUR][1000 genomes]
rs71605686	0.88[EUR][1000 genomes]
rs71605687	0.88[EUR][1000 genomes]
rs71605688	0.85[EUR][1000 genomes]
rs71605691	0.82[EUR][1000 genomes]
rs73838351	0.98[ASN][1000 genomes]
rs7656537	0.95[ASN][1000 genomes]
rs7657443	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7663218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7683045	0.88[EUR][1000 genomes]
rs8180256	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4693788	PTPN13	cis	cerebellum	SCAN
rs4693788	PTPN13	cis	parietal	SCAN
rs4693788	PPM1K	cis	cerebellum	SCAN
rs4693788	PIGY	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87767000-87771000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:87768000-87770800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:87768200-87771400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:87768800-87770600	Enhancers	HMEC	breast
5	chr4:87769000-87770800	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr4:87769200-87770600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:87769200-87771200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:87769400-87770600	Enhancers	Spleen	Spleen
9	chr4:87769600-87770600	Enhancers	NHDF-Ad	bronchial
10	chr4:87769600-87771200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:87769600-87771600	Enhancers	Fetal Muscle Trunk	muscle
12	chr4:87769600-87771600	Flanking Active TSS	NHEK	skin
13	chr4:87769600-87776800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:87769800-87771600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:87769800-87778600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:87770000-87771600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr4:87770200-87770600	Flanking Active TSS	Brain Angular Gyrus	brain
18	chr4:87770200-87770600	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr4:87770200-87770600	Active TSS	Psoas Muscle	Psoas
20	chr4:87770200-87771200	Enhancers	Brain Anterior Caudate	brain
21	chr4:87770200-87771200	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:87770200-87771600	Flanking Active TSS	Hela-S3	cervix
23	chr4:87770200-87776800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:87770400-87770600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr4:87770400-87770800	Active TSS	Right Atrium	heart
26	chr4:87770400-87771000	Weak transcription	Esophagus	oesophagus
27	chr4:87770400-87771200	Enhancers	Brain Substantia Nigra	brain
28	chr4:87770400-87771200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr4:87770400-87771400	Weak transcription	Left Ventricle	heart
30	chr4:87770400-87771800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:87770400-87778600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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