Variant report

Variant	rs2293626
Chromosome Location	chr12:104391041-104391042
allele	C/T
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	EP300	chr12:104391031-104391369	K562	blood:	n/a	chr12:104391154-104391168

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104358555..104361363-chr12:104388778..104391446,2	MCF-7	breast:

Variant related genes	Relation type
GLT8D2	TF binding region
ENSG00000204954	Chromatin interaction
ENSG00000139372	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10507174	1.00[MKK][hapmap]
rs10778307	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861149	0.84[MEX][hapmap]
rs11111864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11553765	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12227567	0.83[MEX][hapmap]
rs12426382	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1550207	1.00[MKK][hapmap]
rs17034637	1.00[MKK][hapmap]
rs17034639	1.00[MKK][hapmap]
rs17034640	1.00[MKK][hapmap]
rs17034642	1.00[MKK][hapmap]
rs17034645	1.00[MKK][hapmap]
rs17034648	1.00[MKK][hapmap]
rs17034662	1.00[MKK][hapmap]
rs17034880	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs17034946	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17034960	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17035056	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs17035129	0.95[AMR][1000 genomes]
rs17035153	0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs17180749	1.00[MKK][hapmap]
rs17192854	1.00[MKK][hapmap]
rs1882019	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2629805	0.99[ASN][1000 genomes]
rs2722200	0.91[ASN][1000 genomes]
rs2888805	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3751207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3751208	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3829300	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4135060	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4135065	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4135076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135078	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4135086	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4135087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4135092	0.83[CEU][hapmap];0.93[GIH][hapmap]
rs4135094	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4135095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4135118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4135131	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4135150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780086	0.87[EUR][1000 genomes]
rs55871448	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55893407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60534873	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs728167	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs7299866	1.00[MKK][hapmap]
rs73390446	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9788014	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs9788136	0.80[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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104362000-104392800	Weak transcription	Fetal Brain Male	brain
2	chr12:104377800-104400200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:104380800-104391400	Weak transcription	Ovary	ovary
4	chr12:104380800-104395600	Weak transcription	Aorta	Aorta
5	chr12:104380800-104400200	Weak transcription	NHLF	lung
6	chr12:104381000-104391200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:104381000-104391200	Weak transcription	Right Ventricle	heart
8	chr12:104381000-104400200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:104381600-104392800	Weak transcription	Left Ventricle	heart
10	chr12:104385000-104400200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:104385400-104400200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:104385600-104404000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:104385800-104400200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:104387000-104400200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:104387200-104404600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:104387400-104391400	Weak transcription	Fetal Stomach	stomach
17	chr12:104388400-104391200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:104388800-104400200	Weak transcription	HSMM	muscle
19	chr12:104390200-104391200	Enhancers	Fetal Heart	heart
20	chr12:104390400-104391600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:104390400-104393000	Enhancers	Fetal Muscle Trunk	muscle
22	chr12:104390600-104391400	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:104390600-104391600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr12:104390800-104391200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:104390800-104391200	Enhancers	HSMMtube	muscle
26	chr12:104390800-104391200	Enhancers	K562	blood
27	chr12:104390800-104391400	Weak transcription	Psoas Muscle	Psoas
28	chr12:104390800-104391800	Enhancers	Fetal Intestine Small	intestine
29	chr12:104390800-104392000	Enhancers	Fetal Lung	lung
30	chr12:104391000-104391200	Enhancers	Colon Smooth Muscle	Colon
31	chr12:104391000-104391400	Active TSS	Right Atrium	heart
32	chr12:104391000-104391600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr12:104391000-104391800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:104391000-104391800	Bivalent Enhancer	HepG2	liver

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