Variant report

Variant	rs12039331
Chromosome Location	chr1:180501196-180501197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180496778..180499562-chr1:180501152..180503837,3	K562	blood:
2	chr1:180491722..180497520-chr1:180497939..180503107,7	MCF-7	breast:
3	chr1:180470259..180473109-chr1:180500598..180503372,2	K562	blood:
4	chr1:180499940..180502814-chr1:180597459..180603584,7	MCF-7	breast:
5	chr1:180491568..180494207-chr1:180499661..180501962,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction
ENSG00000135847	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10737342	0.81[JPT][hapmap]
rs10798761	0.81[JPT][hapmap]
rs10798774	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10913994	0.90[JPT][hapmap]
rs10914002	0.81[JPT][hapmap]
rs10914007	0.94[JPT][hapmap]
rs10914021	0.86[CEU][hapmap]
rs10914022	0.85[CEU][hapmap]
rs10914023	0.84[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs10914034	0.92[EUR][1000 genomes]
rs10914036	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap]
rs12039933	0.90[JPT][hapmap]
rs12041620	0.84[ASN][1000 genomes]
rs12069581	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12136111	0.89[ASN][1000 genomes]
rs12404209	0.90[JPT][hapmap]
rs12405902	0.91[JPT][hapmap]
rs12407684	0.85[CEU][hapmap]
rs12691484	0.81[JPT][hapmap]
rs13374665	0.85[CEU][hapmap]
rs1341924	0.89[JPT][hapmap]
rs1416822	0.86[CEU][hapmap]
rs1416823	0.84[ASN][1000 genomes]
rs1418102	0.81[JPT][hapmap]
rs1538622	0.84[CHB][hapmap]
rs16856086	0.84[ASN][1000 genomes]
rs16856087	0.88[ASN][1000 genomes]
rs16856127	0.90[CEU][hapmap]
rs17300340	0.85[CEU][hapmap]
rs17300579	0.85[CEU][hapmap]
rs17300600	0.88[CEU][hapmap]
rs17300712	0.82[CEU][hapmap]
rs17372295	0.83[CEU][hapmap]
rs17372362	0.85[CEU][hapmap]
rs2877415	0.91[JPT][hapmap]
rs3737584	0.85[JPT][hapmap]
rs3806300	0.81[JPT][hapmap]
rs4405110	0.86[CEU][hapmap]
rs4483365	0.81[JPT][hapmap]
rs4543756	0.90[JPT][hapmap]
rs4642852	0.85[JPT][hapmap]
rs4651068	0.92[EUR][1000 genomes]
rs4652498	0.81[JPT][hapmap]
rs6425625	0.81[JPT][hapmap]
rs6425634	0.91[JPT][hapmap]
rs6425644	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs6425645	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6425646	0.86[CEU][hapmap]
rs6661208	0.81[JPT][hapmap]
rs6680202	0.92[EUR][1000 genomes]
rs6680368	0.81[JPT][hapmap]
rs6692401	0.92[EUR][1000 genomes]
rs6694798	0.89[EUR][1000 genomes]
rs6694975	0.91[EUR][1000 genomes]
rs6695171	0.90[EUR][1000 genomes]
rs6695263	0.92[EUR][1000 genomes]
rs6699076	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6703124	0.91[EUR][1000 genomes]
rs72720922	0.84[ASN][1000 genomes]
rs72720946	0.92[EUR][1000 genomes]
rs72720947	0.93[EUR][1000 genomes]
rs7513944	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs7513963	0.92[EUR][1000 genomes]
rs7515243	0.81[EUR][1000 genomes]
rs7517775	0.85[CEU][hapmap]
rs7517902	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7541993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs7546119	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs7550897	0.92[EUR][1000 genomes]
rs7551178	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs7552084	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs946631	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs946636	0.85[CEU][hapmap]

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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180491600-180511200	Weak transcription	Psoas Muscle	Psoas
2	chr1:180492400-180503000	Weak transcription	Pancreas	Pancrea
3	chr1:180494200-180502200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:180494200-180503000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:180494400-180508200	Weak transcription	Right Ventricle	heart
6	chr1:180494600-180503000	Weak transcription	Fetal Lung	lung
7	chr1:180495000-180502200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:180495000-180503800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:180495200-180502600	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:180496600-180508000	Weak transcription	Right Atrium	heart
11	chr1:180496800-180503600	Weak transcription	Left Ventricle	heart
12	chr1:180497000-180502400	Weak transcription	Fetal Heart	heart
13	chr1:180497000-180502600	Weak transcription	K562	blood
14	chr1:180497800-180511200	Weak transcription	Aorta	Aorta
15	chr1:180498200-180502800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:180499800-180503000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:180500000-180502200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:180500000-180502200	Weak transcription	A549	lung
19	chr1:180500000-180502400	Weak transcription	HepG2	liver
20	chr1:180500000-180503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:180500000-180503400	Weak transcription	Osteobl	bone
22	chr1:180500000-180505200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:180500000-180511200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:180500200-180502200	Weak transcription	HUVEC	blood vessel
25	chr1:180500200-180502800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:180500200-180503000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:180500200-180503000	Weak transcription	Adipose Nuclei	Adipose
28	chr1:180500200-180503400	Weak transcription	HMEC	breast
29	chr1:180500400-180502800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:180500600-180505600	Weak transcription	Placenta	Placenta

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