Variant report

Variant	rs11172891
Chromosome Location	chr12:59449769-59449770
allele	C/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	POLR2A	chr12:59448572-59449918	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr12:59449058-59449776	HCT-116	colon:	n/a	chr12:59449766-59449775
3	FOSL1	chr12:59448986-59449845	HCT-116	colon:	n/a	chr12:59449766-59449775
4	CEBPB	chr12:59449130-59449771	HCT-116	colon:	n/a	chr12:59449548-59449561 chr12:59449711-59449724
5	CEBPB	chr12:59449096-59449787	HCT-116	colon:	n/a	chr12:59449548-59449561 chr12:59449711-59449724

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59312784..59314392-chr12:59448916..59450725,2	MCF-7	breast:
2	chr12:56121872..56123886-chr12:59449553..59451460,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257288	TF binding region
ENSG00000135404	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000139263	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10506357	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877203	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172857	1.00[AFR][1000 genomes]
rs11172858	1.00[AFR][1000 genomes]
rs11172861	1.00[AFR][1000 genomes]
rs11172862	1.00[AFR][1000 genomes]
rs11172868	1.00[AFR][1000 genomes]
rs11172870	0.82[AMR][1000 genomes]
rs11172873	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11172874	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11172876	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172878	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172880	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172881	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172882	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172898	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12367126	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12368035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368658	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422372	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1444099	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1568303	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17536893	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17537939	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17627506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57205785	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58692617	1.00[AFR][1000 genomes]
rs60522760	1.00[AFR][1000 genomes]
rs61919518	1.00[AFR][1000 genomes]
rs61919519	1.00[AFR][1000 genomes]
rs61919520	1.00[AFR][1000 genomes]
rs61919524	1.00[AFR][1000 genomes]
rs61919531	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61919532	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61919550	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61934309	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581224	1.00[AFR][1000 genomes]
rs7138401	1.00[AFR][1000 genomes]
rs7314727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960109	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7968111	1.00[AFR][1000 genomes]
rs7980955	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1047257	chr12:59444966-59520330	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1050662	chr12:59444966-59526442	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59441000-59450800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:59446400-59451000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:59446400-59451200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:59446800-59450000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:59446800-59450200	Enhancers	HMEC	breast
6	chr12:59446800-59450200	Enhancers	NHEK	skin
7	chr12:59448000-59450000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:59448200-59452600	Weak transcription	Fetal Stomach	stomach
9	chr12:59448400-59450000	Enhancers	Hela-S3	cervix
10	chr12:59448400-59453600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:59448600-59450000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:59448600-59450000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:59448600-59450000	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr12:59448600-59451200	Enhancers	HUVEC	blood vessel
15	chr12:59448800-59449800	Enhancers	Osteobl	bone
16	chr12:59448800-59450000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:59448800-59450000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr12:59448800-59450000	Enhancers	HSMMtube	muscle
19	chr12:59448800-59450000	Enhancers	NH-A	brain
20	chr12:59449000-59449800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:59449000-59450000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:59449000-59450000	Enhancers	NHDF-Ad	bronchial
23	chr12:59449000-59459800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:59449200-59449800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:59449200-59449800	Weak transcription	Stomach Mucosa	stomach
26	chr12:59449200-59449800	Flanking Active TSS	A549	lung
27	chr12:59449200-59450000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr12:59449400-59450200	Enhancers	NHLF	lung
29	chr12:59449600-59450400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:59449600-59450800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:59449600-59450800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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