Variant report

Variant	rs8180086
Chromosome Location	chr3:151037880-151037881
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	FOS	chr3:151036661-151038260	MCF10A-Er-Src	breast:	n/a	chr3:151037129-151037138
2	POLR2A	chr3:151036579-151038362	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA3	chr3:151037177-151037930	SK-N-SH	brain:	n/a	chr3:151037890-151037901
4	TCF12	chr3:151037204-151037880	SK-N-SH	brain:	n/a	n/a
5	STAT3	chr3:151036785-151038372	MCF10A-Er-Src	breast:	n/a	chr3:151037531-151037540 chr3:151037886-151037894 chr3:151037650-151037658
6	JUND	chr3:151037203-151038202	SK-N-SH	brain:	n/a	n/a
7	FOS	chr3:151036733-151038284	MCF10A-Er-Src	breast:	n/a	chr3:151037129-151037138
8	STAT3	chr3:151037365-151038281	MCF10A-Er-Src	breast:	n/a	chr3:151037531-151037540 chr3:151037886-151037894 chr3:151037650-151037658
9	FOS	chr3:151037362-151038282	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT1	chr3:151037203-151038653	Hela-S3	cervix:	n/a	chr3:151037531-151037540 chr3:151037886-151037894 chr3:151037650-151037658
11	GATA3	chr3:151037313-151037907	SK-N-SH	brain:	n/a	chr3:151037890-151037901
12	POLR2A	chr3:151036673-151038278	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr3:151036633-151038341	MCF10A-Er-Src	breast:	n/a	chr3:151037531-151037540 chr3:151037886-151037894 chr3:151037650-151037658
14	MYC	chr3:151037489-151038379	MCF10A-Er-Src	breast:	n/a	chr3:151038161-151038177
15	STAT3	chr3:151037400-151038252	MCF10A-Er-Src	breast:	n/a	chr3:151037531-151037540 chr3:151037886-151037894 chr3:151037650-151037658
16	PBX3	chr3:151037360-151037884	SK-N-SH	brain:	n/a	n/a
17	MYC	chr3:151037490-151038382	MCF10A-Er-Src	breast:	n/a	chr3:151038161-151038177
18	TCF12	chr3:151037195-151037952	SK-N-SH	brain:	n/a	n/a
19	FOS	chr3:151036691-151038289	MCF10A-Er-Src	breast:	n/a	chr3:151037129-151037138

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:151037228..151038869-chr3:151040809..151042718,2	MCF-7	breast:

Variant related genes	Relation type
GPR87	TF binding region

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1048408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11714714	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11717955	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11719936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12330831	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12488267	0.88[ASN][1000 genomes]
rs12494865	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1317465	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1352886	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1472122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565574	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16863323	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[ASN][1000 genomes]
rs16863334	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16863336	0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[ASN][1000 genomes]
rs1844924	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1882014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1882015	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1882016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap]
rs1882017	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1920396	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1980143	0.89[CEU][hapmap]
rs28371419	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28497341	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4076581	0.85[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs4475010	0.83[ASN][1000 genomes]
rs4679772	0.89[CEU][hapmap]
rs4679783	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680254	0.82[CEU][hapmap]
rs4680257	0.89[CEU][hapmap]
rs4680260	0.81[CEU][hapmap]
rs56105302	0.96[ASN][1000 genomes]
rs56367650	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58334126	0.94[ASN][1000 genomes]
rs62283021	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6765215	0.97[ASN][1000 genomes]
rs6768130	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6782313	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6807308	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6809692	0.87[CEU][hapmap]
rs7617677	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7621113	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621183	0.84[ASN][1000 genomes]
rs7621211	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7623448	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7653603	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9757688	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9810067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9815520	0.89[CEU][hapmap]
rs9827619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9828553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9829753	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9870740	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9875152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8180086	GPR171	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:151030400-151038400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:151031200-151038200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:151032200-151039200	Enhancers	Hela-S3	cervix
5	chr3:151033000-151038000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:151034600-151039000	Enhancers	NHDF-Ad	bronchial
7	chr3:151034800-151038200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:151035000-151039800	Weak transcription	Placenta	Placenta
9	chr3:151035200-151039600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:151035400-151039000	Enhancers	NHLF	lung
11	chr3:151035800-151038400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:151035800-151038800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr3:151036000-151038600	Enhancers	Osteobl	bone
14	chr3:151036000-151044600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:151036200-151039000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:151036200-151043000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:151036600-151045200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:151037000-151038200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:151037000-151038600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:151037200-151044000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr3:151037400-151038200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:151037400-151038800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:151037400-151039000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:151037600-151038000	Flanking Active TSS	HMEC	breast
25	chr3:151037600-151038000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr3:151037600-151038200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:151037600-151038200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:151037800-151038000	Enhancers	Primary B cells from cord blood	blood
29	chr3:151037800-151038000	Enhancers	NH-A	brain
30	chr3:151037800-151038200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:151037800-151038200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:151037800-151038400	Flanking Active TSS	NHEK	skin
33	chr3:151037800-151039600	Enhancers	Adipose Nuclei	Adipose

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