Variant report

Variant	rs2286041
Chromosome Location	chr12:120527791-120527792
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	NR3C1	chr12:120527532-120527842	A549	lung:	n/a	chr12:120527744-120527751
2	POLR2A	chr12:120527788-120527895	K562	blood:	n/a	n/a
3	POLR2A	chr12:120527520-120530522	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr12:120527691-120528150	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120523806..120527797-chr12:120636547..120640278,4	K562	blood:

Variant related genes	Relation type
CCDC64	TF binding region
ENSG00000255857	Chromatin interaction
ENSG00000089157	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1054631	1.00[ASN][1000 genomes]
rs16949854	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949862	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949870	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613380	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56105460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56152568	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56939014	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57155388	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57339959	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57458743	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59868595	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59911114	0.93[EUR][1000 genomes]
rs60106911	1.00[ASN][1000 genomes]
rs60223336	1.00[ASN][1000 genomes]
rs60590470	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60742518	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61514727	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490279	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6490282	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132099	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7139151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7297564	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298081	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956221	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957325	1.00[AMR][1000 genomes];0.85[EUR][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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120518200-120528600	Weak transcription	Gastric	stomach
2	chr12:120524800-120531000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:120525000-120530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:120525400-120527800	Weak transcription	Spleen	Spleen
5	chr12:120525400-120528200	Weak transcription	Psoas Muscle	Psoas
6	chr12:120525400-120528400	Weak transcription	Esophagus	oesophagus
7	chr12:120525400-120528800	Weak transcription	Lung	lung
8	chr12:120525400-120529600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:120525400-120529800	Weak transcription	Fetal Intestine Large	intestine
10	chr12:120525400-120530200	Weak transcription	Left Ventricle	heart
11	chr12:120525400-120534200	Weak transcription	Right Atrium	heart
12	chr12:120525600-120528000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:120525600-120528000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:120525600-120528000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:120525600-120528200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:120525600-120528600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:120525600-120528600	Weak transcription	Pancreas	Pancrea
18	chr12:120525600-120529000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:120525600-120529200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:120525600-120529200	Weak transcription	Fetal Intestine Small	intestine
21	chr12:120525600-120529400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:120525600-120529400	Weak transcription	Fetal Stomach	stomach
23	chr12:120525600-120529400	Weak transcription	HSMM	muscle
24	chr12:120525600-120529400	Weak transcription	NHLF	lung
25	chr12:120525600-120529600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:120525600-120529600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:120525600-120529800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:120525600-120529800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:120525600-120530000	Weak transcription	Adipose Nuclei	Adipose
30	chr12:120525600-120530000	Weak transcription	Brain Substantia Nigra	brain
31	chr12:120525600-120530200	Weak transcription	Colonic Mucosa	Colon
32	chr12:120525600-120530200	Weak transcription	Right Ventricle	heart
33	chr12:120525600-120530400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:120525600-120530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:120525600-120530400	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:120525600-120531200	Weak transcription	Fetal Lung	lung
37	chr12:120525600-120531400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:120525600-120531600	Weak transcription	Aorta	Aorta
39	chr12:120525600-120531600	Weak transcription	Brain Angular Gyrus	brain
40	chr12:120525600-120531600	Weak transcription	K562	blood
41	chr12:120525600-120532200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:120525600-120532200	Weak transcription	Colon Smooth Muscle	Colon
43	chr12:120525600-120532400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:120525600-120532400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr12:120525600-120532400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:120525600-120532400	Weak transcription	Ovary	ovary
47	chr12:120525600-120532400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:120525600-120533600	Weak transcription	Stomach Mucosa	stomach
49	chr12:120525600-120533600	Weak transcription	HSMMtube	muscle
50	chr12:120525600-120533600	Weak transcription	HUVEC	blood vessel

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