Variant report

Variant	rs12408887
Chromosome Location	chr1:210612839-210612840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:210611698-210614239	IMR90	lung:	n/a	n/a
2	MAX	chr1:210611980-210613201	A549	lung:	n/a	n/a
3	POLR2A	chr1:210612717-210612839	HUVEC	blood vessel:	n/a	n/a
4	TEAD4	chr1:210612206-210613093	SK-N-SH	brain:	n/a	n/a
5	SP1	chr1:210612089-210613096	A549	lung:	n/a	n/a
6	FOSL2	chr1:210612155-210613060	SK-N-SH	brain:	n/a	n/a
7	MAFK	chr1:210612136-210613448	IMR90	lung:	n/a	n/a
8	EP300	chr1:210612017-210613121	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr1:210612003-210613218	SK-N-SH	brain:	n/a	n/a
10	NFIC	chr1:210612072-210613136	SK-N-SH	brain:	n/a	n/a
11	EP300	chr1:210612135-210613075	A549	lung:	n/a	n/a
12	ATF3	chr1:210612405-210612891	A549	lung:	n/a	n/a
13	TCF12	chr1:210612065-210613136	SK-N-SH	brain:	n/a	n/a
14	EP300	chr1:210611954-210613174	A549	lung:	n/a	n/a
15	GABPA	chr1:210612097-210612948	A549	lung:	n/a	n/a
16	TCF12	chr1:210612176-210613005	A549	lung:	n/a	n/a
17	CEBPB	chr1:210612073-210612902	A549	lung:	n/a	n/a
18	RXRA	chr1:210612083-210613097	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr1:210611516-210614181	IMR90	lung:	n/a	n/a
20	GATA3	chr1:210612036-210613265	SK-N-SH	brain:	n/a	n/a
21	FOSL2	chr1:210612077-210613020	A549	lung:	n/a	n/a
22	SP1	chr1:210612022-210613069	A549	lung:	n/a	n/a
23	EBF1	chr1:210612767-210614008	GM12878	blood:	n/a	chr1:210612975-210612986
24	MAX	chr1:210612048-210613046	A549	lung:	n/a	n/a
25	GATA3	chr1:210612023-210613152	SK-N-SH	brain:	n/a	n/a
26	TEAD4	chr1:210612255-210612974	A549	lung:	n/a	n/a
27	MAZ	chr1:210612075-210614083	IMR90	lung:	n/a	n/a
28	PBX3	chr1:210612078-210613098	SK-N-SH	brain:	n/a	n/a
29	TEAD4	chr1:210612207-210613135	A549	lung:	n/a	n/a
30	ATF3	chr1:210612457-210612901	A549	lung:	n/a	n/a
31	EBF1	chr1:210612804-210613088	GM12878	blood:	n/a	chr1:210612975-210612986
32	REST	chr1:210612577-210612844	SK-N-SH	brain:	n/a	n/a
33	TCF12	chr1:210611942-210613155	A549	lung:	n/a	n/a
34	POLR2A	chr1:210612111-210612890	HUVEC	blood vessel:	n/a	n/a
35	PBX3	chr1:210612059-210613098	SK-N-SH	brain:	n/a	n/a
36	FOSL2	chr1:210612134-210612848	SK-N-SH	brain:	n/a	n/a
37	CEBPB	chr1:210612131-210613087	IMR90	lung:	n/a	n/a
38	RAD21	chr1:210612639-210613022	IMR90	lung:	n/a	n/a
39	GATA3	chr1:210612109-210612914	A549	lung:	n/a	n/a
40	GATA3	chr1:210611948-210613213	A549	lung:	n/a	n/a
41	NR3C1	chr1:210612184-210612875	A549	lung:	n/a	n/a
42	POLR2A	chr1:210612162-210612936	SK-N-SH	brain:	n/a	n/a
43	MYC	chr1:210612214-210612909	MCF10A-Er-Src	breast:	n/a	n/a
44	JUND	chr1:210612208-210612856	A549	lung:	n/a	n/a
45	MAX	chr1:210612181-210612942	SK-N-SH	brain:	n/a	n/a
46	MAX	chr1:210612191-210613010	SK-N-SH	brain:	n/a	n/a
47	TEAD4	chr1:210612029-210613113	SK-N-SH	brain:	n/a	n/a
48	JUND	chr1:210612101-210613143	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr1:210612562-210612872	HUVEC	blood vessel:	n/a	n/a
50	JUND	chr1:210612051-210613036	SK-N-SH	brain:	n/a	n/a

No data

Variant related genes	Relation type
HHAT	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11809771	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11810188	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12025108	0.85[AFR][1000 genomes]
rs12119492	0.80[AFR][1000 genomes]
rs2003698	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103692	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2206609	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34549224	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765846	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845015	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845017	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845028	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845030	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845031	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845032	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56252446	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745472	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72745499	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs742562	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527066	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534912	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534914	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs910030	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910031	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910032	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926578	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756883	chr1:210579523-210620779	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	esv2758995	chr1:210579523-210620779	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv515857	chr1:210604130-210613616	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv818811	chr1:210604130-210613616	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1001747	chr1:210604734-210615281	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv999833	chr1:210604734-210620211	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv2421437	chr1:210604746-210613616	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2764216	chr1:210604746-210615293	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210567400-210617200	Weak transcription	Left Ventricle	heart
2	chr1:210571400-210641000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:210592800-210625000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:210602400-210613600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:210609200-210619800	Weak transcription	Esophagus	oesophagus
6	chr1:210610200-210613800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:210610600-210613000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:210610600-210614800	Enhancers	Fetal Muscle Leg	muscle
9	chr1:210610600-210615000	Enhancers	Osteobl	bone
10	chr1:210610800-210614800	Enhancers	NHDF-Ad	bronchial
11	chr1:210611200-210614800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:210611400-210613200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:210611400-210614600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:210611600-210613000	Enhancers	NH-A	brain
15	chr1:210611600-210613600	Enhancers	HUVEC	blood vessel
16	chr1:210611600-210613800	Enhancers	NHLF	lung
17	chr1:210611600-210618400	Weak transcription	Thymus	Thymus
18	chr1:210611600-210639600	Weak transcription	Aorta	Aorta
19	chr1:210611800-210614200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:210611800-210614200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:210611800-210614200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:210611800-210614600	Enhancers	A549	lung
23	chr1:210611800-210614600	Enhancers	HMEC	breast
24	chr1:210611800-210614800	Enhancers	NHEK	skin
25	chr1:210612000-210613800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:210612000-210615000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:210612200-210613000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:210612200-210613000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr1:210612200-210613200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:210612200-210613200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:210612200-210613600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:210612200-210613800	Enhancers	Fetal Muscle Trunk	muscle
33	chr1:210612200-210614600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:210612400-210613000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:210612400-210613000	Enhancers	Fetal Lung	lung
36	chr1:210612400-210613200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:210612400-210613800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:210612600-210613000	Enhancers	Fetal Heart	heart
39	chr1:210612600-210613200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr1:210612600-210613800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:210612600-210618400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:210612800-210613600	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr1:210612800-210613600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:210612800-210614800	Flanking Active TSS	HSMMtube	muscle
45	chr1:210612800-210615000	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links