Variant report

Variant	rs12061213
Chromosome Location	chr1:211816546-211816547
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	FOXA1	chr1:211816510-211816973	HepG2	liver:	n/a	n/a
2	TCF7L2	chr1:211816461-211817510	PANC-1	pancreas:	n/a	chr1:211817379-211817389 chr1:211816835-211816851 chr1:211816835-211816851 chr1:211816839-211816848
3	HDAC2	chr1:211816525-211817537	HepG2	liver:	n/a	chr1:211816752-211816760 chr1:211817165-211817184
4	EP300	chr1:211816493-211817563	HepG2	liver:	n/a	chr1:211817303-211817313 chr1:211817067-211817083
5	REST	chr1:211816523-211817047	HepG2	liver:	n/a	chr1:211816967-211816981
6	POLR2A	chr1:211815491-211817685	Hela-S3	cervix:	n/a	n/a
7	MYBL2	chr1:211816402-211817054	HepG2	liver:	n/a	n/a
8	STAT1	chr1:211816244-211817683	Hela-S3	cervix:	n/a	chr1:211817011-211817023 chr1:211817319-211817327 chr1:211817317-211817328 chr1:211817577-211817588
9	CTCF	chr1:211816520-211816670	HAc	cerebellar:	n/a	n/a
10	POLR2A	chr1:211816536-211817487	HepG2	liver:	n/a	n/a
11	MBD4	chr1:211816513-211817037	HepG2	liver:	n/a	n/a
12	FOXA1	chr1:211816462-211817492	HepG2	liver:	n/a	n/a
13	TCF7L2	chr1:211816444-211817131	HepG2	liver:	n/a	chr1:211816835-211816851 chr1:211816835-211816851 chr1:211816839-211816848
14	NFIC	chr1:211816531-211817452	HepG2	liver:	n/a	n/a
15	RXRA	chr1:211816509-211817124	HepG2	liver:	n/a	chr1:211816750-211816759
16	NR2F2	chr1:211816439-211817276	HepG2	liver:	n/a	n/a
17	NFIC	chr1:211816493-211817587	HepG2	liver:	n/a	n/a
18	FOXA1	chr1:211816541-211817069	HepG2	liver:	n/a	n/a
19	SMARCB1	chr1:211816234-211817602	Hela-S3	cervix:	n/a	n/a
20	MYBL2	chr1:211816431-211817430	HepG2	liver:	n/a	n/a
21	TEAD4	chr1:211816467-211817345	HepG2	liver:	n/a	n/a
22	RXRA	chr1:211816521-211817058	HepG2	liver:	n/a	chr1:211816750-211816759
23	HNF4G	chr1:211816541-211816978	HepG2	liver:	n/a	n/a
24	EP300	chr1:211816483-211817045	HepG2	liver:	n/a	n/a
25	SMARCC1	chr1:211815965-211817609	Hela-S3	cervix:	n/a	n/a
26	SP1	chr1:211816542-211817096	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:211750794..211754252-chr1:211815868..211819773,4	MCF-7	breast:
2	chr1:211749200..211754595-chr1:211816014..211824648,8	K562	blood:

Variant related genes	Relation type
ENSG00000228792	TF binding region
ENSG00000170385	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11119781	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12059593	1.00[EUR][1000 genomes]
rs12059673	1.00[EUR][1000 genomes]
rs12069828	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084324	1.00[EUR][1000 genomes]
rs12085440	1.00[EUR][1000 genomes]
rs12085684	1.00[EUR][1000 genomes]
rs12086556	1.00[EUR][1000 genomes]
rs12089298	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17017861	1.00[EUR][1000 genomes]
rs28463715	1.00[EUR][1000 genomes]
rs55635902	1.00[EUR][1000 genomes]
rs55766448	1.00[EUR][1000 genomes]
rs55860373	1.00[EUR][1000 genomes]
rs56299016	1.00[EUR][1000 genomes]
rs58355459	1.00[EUR][1000 genomes]
rs73073399	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075304	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075309	1.00[EUR][1000 genomes]

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	nsv1010919	chr1:211804252-211823073	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211804200-211816600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:211807200-211816600	Weak transcription	Right Ventricle	heart
3	chr1:211807200-211817200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:211807400-211816800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:211807600-211816600	Weak transcription	Left Ventricle	heart
6	chr1:211811400-211829600	Enhancers	Fetal Intestine Small	intestine
7	chr1:211811600-211828200	Enhancers	Fetal Intestine Large	intestine
8	chr1:211812400-211816600	Weak transcription	Adipose Nuclei	Adipose
9	chr1:211812600-211816600	Weak transcription	Esophagus	oesophagus
10	chr1:211813200-211816600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:211813200-211817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:211813600-211816600	Weak transcription	Placenta	Placenta
13	chr1:211813600-211817200	Weak transcription	HSMM	muscle
14	chr1:211813600-211821600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:211813800-211816600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:211813800-211816800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:211813800-211817000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:211813800-211822600	Weak transcription	NHDF-Ad	bronchial
19	chr1:211814000-211816800	Weak transcription	HUVEC	blood vessel
20	chr1:211814000-211817000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:211814000-211817000	Weak transcription	Osteobl	bone
22	chr1:211814200-211816800	Weak transcription	NHLF	lung
23	chr1:211814600-211818600	Flanking Active TSS	Hela-S3	cervix
24	chr1:211815000-211816600	Weak transcription	Liver	Liver
25	chr1:211816000-211817000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr1:211816000-211817400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:211816000-211817600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:211816000-211818000	Enhancers	Fetal Thymus	thymus
29	chr1:211816000-211818400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr1:211816200-211817000	Enhancers	Colonic Mucosa	Colon
31	chr1:211816200-211817400	Enhancers	Lung	lung
32	chr1:211816200-211817600	Enhancers	Brain Hippocampus Middle	brain
33	chr1:211816200-211817600	Enhancers	Fetal Muscle Leg	muscle
34	chr1:211816200-211817600	Enhancers	Ovary	ovary
35	chr1:211816200-211817600	Enhancers	Pancreas	Pancrea
36	chr1:211816200-211817600	Enhancers	Stomach Mucosa	stomach
37	chr1:211816200-211817800	Flanking Active TSS	HepG2	liver
38	chr1:211816200-211818600	Enhancers	Duodenum Mucosa	Duodenum
39	chr1:211816200-211819400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:211816400-211816800	Enhancers	A549	lung
41	chr1:211816400-211817000	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr1:211816400-211817200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:211816400-211817400	Enhancers	Fetal Heart	heart
44	chr1:211816400-211817600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:211816400-211817600	Enhancers	Gastric	stomach
46	chr1:211816400-211817600	Enhancers	Spleen	Spleen
47	chr1:211816400-211817600	Enhancers	NH-A	brain
48	chr1:211816400-211817800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:211816400-211817800	Enhancers	HMEC	breast
50	chr1:211816400-211817800	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links