Variant report

Variant	rs2219382
Chromosome Location	chr12:10771779-10771780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:10771079..10773905-chr12:10786792..10788770,2	K562	blood:
2	chr12:10765155..10768386-chr12:10770513..10774457,4	MCF-7	breast:
3	chr12:10770924..10772839-chr12:10825568..10827149,2	MCF-7	breast:
4	chr12:10770221..10774557-chr12:10774772..10778392,5	K562	blood:

Variant related genes	Relation type
ENSG00000111196	Chromatin interaction
ENSG00000060140	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10083164	0.83[JPT][hapmap]
rs1026442	1.00[JPT][hapmap]
rs10431297	0.82[JPT][hapmap]
rs1054396	0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs1073305	0.82[JPT][hapmap]
rs10743911	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10772334	1.00[JPT][hapmap]
rs10772340	0.82[JPT][hapmap]
rs10772343	0.81[JPT][hapmap]
rs10772347	0.82[JPT][hapmap]
rs10845180	1.00[JPT][hapmap]
rs10845181	0.82[JPT][hapmap]
rs10845184	0.92[ASN][1000 genomes]
rs10845185	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10845192	0.82[JPT][hapmap]
rs10845194	0.81[JPT][hapmap]
rs10845195	0.82[JPT][hapmap]
rs10845197	0.80[JPT][hapmap]
rs10845198	0.82[JPT][hapmap]
rs11053877	1.00[JPT][hapmap]
rs11053880	1.00[JPT][hapmap]
rs11053881	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11053882	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12306757	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12306815	0.81[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12811247	1.00[JPT][hapmap]
rs1870194	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2125091	0.94[JPT][hapmap]
rs2290718	1.00[JPT][hapmap]
rs2305853	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2418087	0.82[JPT][hapmap]
rs2418088	0.82[JPT][hapmap]
rs2900467	0.86[MEX][hapmap];0.85[AMR][1000 genomes]
rs2900513	0.82[JPT][hapmap]
rs3759264	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3759265	0.93[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782674	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6488316	0.82[JPT][hapmap]
rs7312261	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7313620	0.81[JPT][hapmap]
rs7350557	0.82[JPT][hapmap]
rs7350597	0.82[JPT][hapmap]
rs755498	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7968284	0.82[JPT][hapmap]
rs7968819	0.80[ASN][1000 genomes]
rs7971142	0.82[JPT][hapmap]
rs897880	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs897882	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9988929	0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832329	chr12:10677094-10845946	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2219382	TPI1	cis	parietal	SCAN
rs2219382	GPRC5A	cis	parietal	SCAN
rs2219382	NOP2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10766600-10787000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:10766600-10789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:10766600-10794400	Weak transcription	Gastric	stomach
4	chr12:10766800-10789400	Weak transcription	Esophagus	oesophagus
5	chr12:10767000-10772400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:10767000-10772400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:10767000-10778400	Weak transcription	Colonic Mucosa	Colon
8	chr12:10767200-10772000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr12:10767200-10772200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:10767200-10775000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:10767200-10780600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:10767200-10781200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:10767400-10772400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:10767600-10776800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:10769600-10772400	Enhancers	NHDF-Ad	bronchial
16	chr12:10770000-10772000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:10770000-10772400	Enhancers	HSMM	muscle
18	chr12:10770200-10772000	Enhancers	NHEK	skin
19	chr12:10770200-10772400	Enhancers	HMEC	breast
20	chr12:10770200-10773000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:10770200-10774600	Enhancers	HSMMtube	muscle
22	chr12:10770400-10771800	Genic enhancers	HUVEC	blood vessel
23	chr12:10770400-10771800	Enhancers	Osteobl	bone
24	chr12:10770400-10772000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:10770600-10771800	Enhancers	NHLF	lung
26	chr12:10770600-10773000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:10770600-10777600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:10771000-10772000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr12:10771200-10772400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:10771200-10776000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr12:10771400-10782200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:10771600-10771800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:10771600-10772400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:10771600-10772800	Weak transcription	K562	blood
35	chr12:10771600-10773200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:10771600-10775800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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