Variant report

Variant	rs12188654
Chromosome Location	chr5:49952847-49952848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:49951146..49952897-chr5:49957210..49959408,2	MCF-7	breast:
2	chr5:49951637..49953470-chr5:49962458..49964484,2	MCF-7	breast:
3	chr5:49951519..49954288-chr5:49991653..49994102,2	MCF-7	breast:
4	chr5:49952103..49954206-chr5:49962638..49964353,2	MCF-7	breast:
5	chr5:49951565..49954104-chr5:49960060..49962047,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151883	Chromatin interaction
ENSG00000271752	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10035164	1.00[CHB][hapmap]
rs10036060	1.00[CHB][hapmap]
rs10038842	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10039272	0.84[ASN][1000 genomes]
rs10039639	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs10041633	0.82[EUR][1000 genomes]
rs10043477	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10044566	1.00[CHB][hapmap]
rs10051561	0.84[ASN][1000 genomes]
rs10052001	0.84[EUR][1000 genomes]
rs10053011	1.00[CHB][hapmap]
rs10054381	1.00[CHB][hapmap]
rs10056836	1.00[CHB][hapmap]
rs10058388	0.88[ASN][1000 genomes]
rs10059085	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10065069	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10065432	0.84[ASN][1000 genomes]
rs10070517	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10072398	0.84[ASN][1000 genomes]
rs10075034	1.00[CHB][hapmap]
rs10085036	1.00[CHB][hapmap]
rs10434558	1.00[CEU][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap]
rs10471940	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10471956	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10755235	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10940424	0.82[EUR][1000 genomes]
rs10940472	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10940497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11738761	0.82[EUR][1000 genomes]
rs11739828	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11741205	0.82[EUR][1000 genomes]
rs11745945	0.82[EUR][1000 genomes]
rs11750241	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11750771	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12188262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12519006	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12521579	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12653803	0.81[ASN][1000 genomes]
rs12654776	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13153982	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13162921	0.81[EUR][1000 genomes]
rs13164951	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13173734	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13359044	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1375127	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs152102	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs154133	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs154134	0.88[ASN][1000 genomes]
rs154135	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs154137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs154138	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs154140	0.88[ASN][1000 genomes]
rs154141	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs157970	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16884018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169497	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[ASN][1000 genomes]
rs171555	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17195388	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs182230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1823262	0.86[EUR][1000 genomes]
rs1823263	0.81[ASN][1000 genomes]
rs1839128	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1900738	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1972980	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1988613	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2034392	0.80[EUR][1000 genomes]
rs2034393	0.82[EUR][1000 genomes]
rs2034394	0.81[EUR][1000 genomes]
rs2121979	0.82[EUR][1000 genomes]
rs2166893	0.82[EUR][1000 genomes]
rs2166894	0.82[EUR][1000 genomes]
rs2354526	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548581	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2548582	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2548583	0.83[CEU][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs256340	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs256341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2594706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs26062	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs26065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26066	0.84[EUR][1000 genomes]
rs26068	1.00[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs26069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26071	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2697662	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs27244	0.82[EUR][1000 genomes]
rs27245	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs27251	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs27254	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27357	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27389	1.00[CHB][hapmap]
rs27465	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27466	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs27467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs27468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27627	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27725	0.81[EUR][1000 genomes]
rs28085	0.81[EUR][1000 genomes]
rs282549	0.84[EUR][1000 genomes]
rs282550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282551	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282552	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs282553	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs282557	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs282559	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs282561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28505342	0.84[ASN][1000 genomes]
rs28711235	0.84[ASN][1000 genomes]
rs32376	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs32377	0.84[EUR][1000 genomes]
rs32378	0.84[EUR][1000 genomes]
rs32404	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap]
rs32425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3763367	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs39949	0.81[ASN][1000 genomes]
rs4029420	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs42284	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4440312	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4865628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4865895	0.82[EUR][1000 genomes]
rs57079776	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578198	0.91[CEU][hapmap]
rs62366937	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450292	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6450301	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450359	1.00[CEU][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6868550	0.84[ASN][1000 genomes]
rs6869356	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6872070	0.82[EUR][1000 genomes]
rs6872496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6879306	0.82[EUR][1000 genomes]
rs6886872	0.92[EUR][1000 genomes]
rs6888147	0.84[EUR][1000 genomes]
rs6890519	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6890869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73097023	0.88[ASN][1000 genomes]
rs7449019	0.91[EUR][1000 genomes]
rs7702541	0.81[ASN][1000 genomes]
rs7709831	0.84[EUR][1000 genomes]
rs7710150	0.84[EUR][1000 genomes]
rs7711839	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7721050	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7723361	0.91[CEU][hapmap]
rs7728222	0.82[EUR][1000 genomes]
rs7730847	0.82[EUR][1000 genomes]
rs7734389	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7736142	0.81[ASN][1000 genomes]
rs895801	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs921210	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS 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	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12188654	PARP8	Cis_1M	lymphoblastoid	RTeQTL
rs12188654	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49949800-49961600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:49950000-49959400	Weak transcription	Primary T cells from cord blood	blood
3	chr5:49950200-49959200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:49951000-49953200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr5:49951200-49953400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr5:49951200-49954000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr5:49951800-49954000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:49951800-49954000	Weak transcription	Primary B cells from cord blood	blood
9	chr5:49952000-49953200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:49952000-49954000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr5:49952600-49953000	Enhancers	Stomach Mucosa	stomach
12	chr5:49952800-49953000	Enhancers	Esophagus	oesophagus
13	chr5:49952800-49953200	Active TSS	Pancreatic Islets	Pancreatic Islet

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