Variant report

Variant	rs4366490
Chromosome Location	chr11:62912854-62912855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr11:62912803-62913496	SK-N-SH	brain:	n/a	n/a
2	GATA2	chr11:62912376-62913361	HUVEC	blood vessel:	n/a	chr11:62913069-62913079
3	FOS	chr11:62912738-62913506	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr11:62912769-62913391	HUVEC	blood vessel:	n/a	n/a
5	NFIC	chr11:62912804-62913336	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:62912823-62912873	GM19239	blood:	n/a
2	chr11:62912823-62912873	HPAEpiC	pulmonary alveolar:	n/a
3	chr11:62912823-62912873	CMK	blood:	n/a
4	chr11:62912823-62912873	GM06990	blood:	n/a
5	chr11:62912823-62912873	BE2_C	brain:	n/a
6	chr11:62912823-62912873	HCT-116	colon:	n/a
7	chr11:62912823-62912873	PANC-1	pancreas:	n/a
8	chr11:62912823-62912873	Hela-S3	cervix:	n/a
9	chr11:62912823-62912873	HepG2	liver:	n/a
10	chr11:62912823-62912873	NHDF-neo	bronchial:	n/a
11	chr11:62912823-62912873	SK-N-MC	brain:	n/a
12	chr11:62912823-62912873	HAEpiC	amniotic membrane:	n/a
13	chr11:62912823-62912873	ECC-1	luminal epithelium:	n/a
14	chr11:62912823-62912873	SKMC	muscle:	n/a
15	chr11:62912823-62912873	Hepatocyte	liver:	n/a
16	chr11:62912823-62912873	NB4	blood:	n/a
17	chr11:62912823-62912873	Jurkat	blood:	n/a
18	chr11:62912823-62912873	HRCEpiC	kidney:	n/a
19	chr11:62912823-62912873	ovcar-3	ovarian:	n/a
20	chr11:62912823-62912873	PFSK-1	brain:	n/a
21	chr11:62912823-62912873	HCM	heart:	n/a
22	chr11:62912823-62912873	LNCaP	prostate:	n/a
23	chr11:62912823-62912873	HL-60	blood:	n/a
24	chr11:62912823-62912873	GM12878	blood:	n/a
25	chr11:62912823-62912873	AG04449	skin:	fetal
26	chr11:62912823-62912873	NT2-D1	testis:	n/a
27	chr11:62912823-62912873	BJ	skin:	n/a
28	chr11:62912823-62912873	IMR90	lung:	fetal
29	chr11:62912823-62912873	HRPEpiC	eye:	n/a
30	chr11:62912823-62912873	GM12892	blood:	n/a
31	chr11:62912823-62912873	MCF-7	breast:	n/a
32	chr11:62912823-62912873	SAEC	small airway:	n/a
33	chr11:62912823-62912873	HCF	heart:	n/a
34	chr11:62912823-62912873	RPTEC	kidney:	n/a
35	chr11:62912823-62912873	AG04450	lung:	fetal
36	chr11:62912823-62912873	HUVEC	blood vessel:	n/a
37	chr11:62912823-62912873	NHBE	bronchial:	n/a
38	chr11:62912823-62912873	ProgFib	skin:	n/a
39	chr11:62912823-62912873	PrEC	prostate:	n/a
40	chr11:62912823-62912873	T-47D	breast:	n/a
41	chr11:62912823-62912873	AG09309	skin:	n/a
42	chr11:62912823-62912873	SK-N-SH	brain:	n/a
43	chr11:62912823-62912873	A549	lung:	n/a
44	chr11:62912823-62912873	HEK293	kidney:	embryo
45	chr11:62912823-62912873	HNPCEpiC	eye:	n/a
46	chr11:62912823-62912873	NH-A	brain:	n/a
47	chr11:62912823-62912873	HCPEpiC	choroid plexus:	n/a
48	chr11:62912823-62912873	MCF10A-Er-Src	breast:	n/a
49	chr11:62912823-62912873	GM12891	blood:	n/a
50	chr11:62912823-62912873	HMEC	breast:	n/a

No data

Variant related genes	Relation type
SLC22A24	TF binding region
SLC22A24	CpG island

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10736724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11231322	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11231373	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11231374	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11231375	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11231379	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12364908	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1939743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1939747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939750	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1939752	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1939753	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1939757	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1939758	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1939770	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2105623	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2155325	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4121458	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4297470	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4345971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4393318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4405319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4963246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs4963247	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4963248	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6591763	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6591764	0.81[ASN][1000 genomes]
rs7106537	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7948969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7952201	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs948060	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34011	chr11:62652779-62993702	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1045308	chr11:62803635-63109338	Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv541059	chr11:62803635-63109338	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv897626	chr11:62839667-62967791	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv555177	chr11:62847518-63110569	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1049725	chr11:62848172-63057827	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv541060	chr11:62848172-63057827	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1047571	chr11:62848172-63109338	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv430397	chr11:62852616-63072310	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv430398	chr11:62881839-62914202	Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv2755674	chr11:62883681-62913852	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv430399	chr11:62883681-62913852	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	esv2753282	chr11:62883681-62986146	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv975391	chr11:62910820-62917965	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Conotruncal heart defects	24800985	GWAS catalog

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62911400-62914400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr11:62911800-62913200	Enhancers	HUVEC	blood vessel
3	chr11:62912400-62913400	Enhancers	Left Ventricle	heart
4	chr11:62912600-62913000	Enhancers	Adipose Nuclei	Adipose
5	chr11:62912600-62913600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links