Variant report

Variant	rs1054442
Chromosome Location	chr12:49389320-49389321
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:235)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:235 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:49389300-49389450	Hela-S3	cervix:	n/a	n/a
2	BACH1	chr12:49388935-49389591	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr12:49389080-49389685	MCF-7	breast:	n/a	n/a
4	CTCF	chr12:49389280-49389430	HA-sp	spinal cord:	n/a	n/a
5	CTCF	chr12:49389139-49389552	A549	lung:	n/a	n/a
6	SMC3	chr12:49388909-49389765	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr12:49389233-49389460	K562	blood:	n/a	n/a
8	CTCF	chr12:49389211-49389551	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr12:49389320-49389470	HRPEpiC	eye:	n/a	n/a
10	CTCF	chr12:49389234-49389543	Spleen_OC	spleen:	n/a	n/a
11	CTCF	chr12:49389300-49389450	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr12:49389136-49389496	A549	lung:	n/a	n/a
13	CTCF	chr12:49389171-49389528	A549	lung:	n/a	n/a
14	MAFK	chr12:49389251-49389451	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr12:49389074-49389562	K562	blood:	n/a	n/a
16	CTCF	chr12:49389280-49389430	HCM	heart:	n/a	n/a
17	CTCF	chr12:49389160-49389530	SK-N-SH_RA	brain:	n/a	n/a
18	JUND	chr12:49389269-49389559	K562	blood:	n/a	n/a
19	RAD21	chr12:49389148-49389578	HepG2	liver:	n/a	n/a
20	NRF1	chr12:49389213-49389369	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr12:49389172-49389587	T-47D	breast:	n/a	n/a
22	CTCF	chr12:49389300-49389450	GM12865	blood:	n/a	n/a
23	RAD21	chr12:49389166-49389592	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr12:49389300-49389450	GM12869	blood:	n/a	n/a
25	SMC3	chr12:49389206-49389560	GM12878	blood:	n/a	n/a
26	RAD21	chr12:49389177-49389554	GM12878	blood:	n/a	n/a
27	CTCF	chr12:49389300-49389450	BE2_C	brain:	n/a	n/a
28	CTCF	chr12:49389246-49389511	LNCaP	prostate:	n/a	n/a
29	YY1	chr12:49389168-49389441	GM12892	blood:	n/a	n/a
30	MXI1	chr12:49389157-49389526	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr12:49389131-49389535	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr12:49388938-49389858	HCT-116	colon:	n/a	n/a
33	CTCF	chr12:49389107-49389613	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr12:49389231-49389521	NHEK	skin:	n/a	n/a
35	RAD21	chr12:49389169-49389646	ECC-1	luminal epithelium:	n/a	n/a
36	CTCF	chr12:49389269-49389505	MCF-7	breast:	n/a	n/a
37	RAD21	chr12:49389197-49389556	A549	lung:	n/a	n/a
38	CTCF	chr12:49389280-49389430	GM12865	blood:	n/a	n/a
39	POLR2A	chr12:49389097-49389565	SK-N-MC	brain:	n/a	n/a
40	CTCF	chr12:49389259-49389509	Lung_OC	lung:	n/a	n/a
41	CTCF	chr12:49389277-49389485	GM13976	blood:	n/a	n/a
42	CTCF	chr12:49389294-49389506	GM20000	blood:	n/a	n/a
43	MYC	chr12:49389309-49389657	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr12:49389251-49389516	GM19239	blood:	n/a	n/a
45	CTCF	chr12:49389270-49389497	HepG2	liver:	n/a	n/a
46	TEAD4	chr12:49389211-49389680	H1-hESC	embryonic stem cell:	n/a	n/a
47	CHD2	chr12:49389202-49389488	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr12:49389241-49389526	MCF-7	breast:	n/a	n/a
49	CTCF	chr12:49389320-49389470	HEEpiC	esophagus:	n/a	n/a
50	RAD21	chr12:49389037-49389703	A549	lung:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49370543..49373211-chr12:49387729..49389906,2	K562	blood:
2	chr12:49329635..49330325-chr12:49389189..49389770,2	MCF-7	breast:
3	chr12:49365293..49369225-chr12:49386844..49389863,3	MCF-7	breast:
4	chr12:49371444..49371981-chr12:49389232..49389805,2	K562	blood:
5	chr12:49366496..49367129-chr12:49388953..49389723,2	MCF-7	breast:
6	chr12:49387824..49389394-chr12:49523578..49525340,2	K562	blood:
7	chr12:49349915..49351718-chr12:49389253..49391123,2	MCF-7	breast:
8	chr12:49363715..49365253-chr12:49387524..49389322,2	MCF-7	breast:
9	chr12:49370543..49373352-chr12:49387358..49390310,3	K562	blood:
10	chr12:49246756..49247834-chr12:49389266..49390145,3	K562	blood:
11	chr12:49367583..49368499-chr12:49388939..49389819,2	K562	blood:
12	chr12:49388997..49391311-chr12:49485672..49487857,2	K562	blood:
13	chr12:49350460..49352797-chr12:49389222..49392992,4	MCF-7	breast:
14	chr12:49388402..49390811-chr12:49410964..49413711,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257913	TF binding region
ENSG00000181929	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000125084	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000169884	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10459221	0.80[ASN][1000 genomes]
rs10459232	0.85[CEU][hapmap];0.80[ASN][1000 genomes]
rs10747559	0.83[ASN][1000 genomes]
rs10783299	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs10783300	0.96[ASN][1000 genomes]
rs10783301	0.86[ASN][1000 genomes]
rs10875906	0.97[ASN][1000 genomes]
rs10875908	0.96[ASN][1000 genomes]
rs10875910	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10875911	0.96[ASN][1000 genomes]
rs10875912	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10875913	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10875914	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs10875915	0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10875917	0.80[ASN][1000 genomes]
rs11168822	0.94[ASN][1000 genomes]
rs11168827	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11168838	0.80[ASN][1000 genomes]
rs11168839	0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168850	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1138908	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11614738	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12580349	0.93[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2117029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2241726	0.93[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2293445	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[ASN][1000 genomes]
rs2293446	0.96[ASN][1000 genomes]
rs2304275	0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs34436857	0.87[ASN][1000 genomes]
rs3741619	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741622	0.89[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3782357	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6580698	0.85[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6580699	0.85[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7296288	0.84[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs7969091	0.85[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs876333	0.92[ASN][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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1054442	RHEBL1	cis	cerebellum	SCAN
rs1054442	FKBP11	cis	parietal	SCAN
rs1054442	H1FNT	cis	parietal	SCAN
rs1054442	FKBP11	cis	cerebellum	SCAN
rs1054442	RHEBL1	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49388200-49390000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
2	chr12:49388200-49390600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:49388200-49393600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:49388400-49389400	Active TSS	Right Atrium	heart
5	chr12:49388400-49389800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:49388600-49389400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr12:49388600-49389400	Active TSS	Right Ventricle	heart
8	chr12:49388600-49389600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:49388600-49390400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:49388800-49389400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
11	chr12:49388800-49389400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:49388800-49389400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:49388800-49389400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:49388800-49389400	Bivalent Enhancer	Liver	Liver
15	chr12:49388800-49389400	Bivalent Enhancer	Fetal Stomach	stomach
16	chr12:49388800-49389400	Flanking Active TSS	Hela-S3	cervix
17	chr12:49388800-49389400	Enhancers	HMEC	breast
18	chr12:49388800-49389400	Bivalent Enhancer	HSMM	muscle
19	chr12:49388800-49389600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:49388800-49389600	Bivalent Enhancer	Fetal Thymus	thymus
21	chr12:49388800-49389600	Bivalent Enhancer	NH-A	brain
22	chr12:49388800-49389800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:49388800-49389800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:49388800-49389800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr12:49388800-49390400	Bivalent Enhancer	Brain Germinal Matrix	brain
26	chr12:49389000-49389400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr12:49389000-49389400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
28	chr12:49389000-49389400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
29	chr12:49389000-49389400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
30	chr12:49389000-49389400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr12:49389000-49389400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
32	chr12:49389000-49389400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
33	chr12:49389000-49389400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:49389000-49389400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:49389000-49389400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:49389000-49389400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
37	chr12:49389000-49389400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
38	chr12:49389000-49389400	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr12:49389000-49389400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr12:49389000-49389400	Enhancers	Brain Substantia Nigra	brain
41	chr12:49389000-49389400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
42	chr12:49389000-49389400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
43	chr12:49389000-49389400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
44	chr12:49389000-49389400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
45	chr12:49389000-49389400	Flanking Active TSS	A549	lung
46	chr12:49389000-49389400	Flanking Active TSS	HSMMtube	muscle
47	chr12:49389000-49389400	Active TSS	K562	blood
48	chr12:49389000-49389600	Bivalent Enhancer	Primary B cells from cord blood	blood
49	chr12:49389000-49389600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
50	chr12:49389000-49389600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links