Variant report

Variant	rs6542056
Chromosome Location	chr2:113192136-113192137
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:113192114-113192164	HUVEC	blood vessel:	n/a
2	chr2:113192114-113192164	HCF	heart:	n/a
3	chr2:113192114-113192164	GM12891	blood:	n/a
4	chr2:113192114-113192164	SAEC	small airway:	n/a
5	chr2:113192114-113192164	MCF-7	breast:	n/a
6	chr2:113192114-113192164	BJ	skin:	n/a
7	chr2:113192114-113192164	AG09319	gingival:	n/a
8	chr2:113192114-113192164	NHBE	bronchial:	n/a
9	chr2:113192114-113192164	SK-N-SH_RA	brain:	n/a
10	chr2:113192114-113192164	HRCEpiC	kidney:	n/a
11	chr2:113192114-113192164	HCM	heart:	n/a
12	chr2:113192114-113192164	NHDF-neo	bronchial:	n/a
13	chr2:113192114-113192164	HRPEpiC	eye:	n/a
14	chr2:113192114-113192164	Hela-S3	cervix:	n/a
15	chr2:113192114-113192164	ECC-1	luminal epithelium:	n/a
16	chr2:113192114-113192164	PANC-1	pancreas:	n/a
17	chr2:113192114-113192164	AG09309	skin:	n/a
18	chr2:113192114-113192164	T-47D	breast:	n/a
19	chr2:113192114-113192164	PFSK-1	brain:	n/a
20	chr2:113192114-113192164	NH-A	brain:	n/a
21	chr2:113192114-113192164	ProgFib	skin:	n/a
22	chr2:113192114-113192164	HRE	kidney:	n/a
23	chr2:113192114-113192164	SKMC	muscle:	n/a
24	chr2:113192114-113192164	Hepatocyte	liver:	n/a
25	chr2:113192114-113192164	HL-60	blood:	n/a
26	chr2:113192114-113192164	HEEpiC	esophagus:	n/a
27	chr2:113192114-113192164	AG04450	lung:	fetal
28	chr2:113192114-113192164	SK-N-SH	brain:	n/a
29	chr2:113192114-113192164	AG10803	skin:	n/a
30	chr2:113192114-113192164	GM19239	blood:	n/a
31	chr2:113192114-113192164	HIPEpiC	eye:	n/a
32	chr2:113192114-113192164	A549	lung:	n/a
33	chr2:113192114-113192164	HMEC	breast:	n/a
34	chr2:113192114-113192164	U87	brain:	n/a
35	chr2:113192114-113192164	NB4	blood:	n/a
36	chr2:113192114-113192164	K562	blood:	n/a
37	chr2:113192114-113192164	HCT-116	colon:	n/a
38	chr2:113192114-113192164	CMK	blood:	n/a
39	chr2:113192114-113192164	NT2-D1	testis:	n/a
40	chr2:113192114-113192164	GM12878	blood:	n/a
41	chr2:113192114-113192164	GM06990	blood:	n/a
42	chr2:113192114-113192164	SK-N-MC	brain:	n/a
43	chr2:113192114-113192164	MCF10A-Er-Src	breast:	n/a
44	chr2:113192114-113192164	HepG2	liver:	n/a
45	chr2:113192114-113192164	PrEC	prostate:	n/a
46	chr2:113192114-113192164	BE2_C	brain:	n/a
47	chr2:113192114-113192164	Caco-2	colon:	n/a
48	chr2:113192114-113192164	IMR90	lung:	fetal
49	chr2:113192114-113192164	LNCaP	prostate:	n/a
50	chr2:113192114-113192164	GM12892	blood:	n/a

No data

Variant related genes	Relation type
RGPD8	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11682795	1.00[CEU][hapmap]
rs11685514	1.00[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs11688511	1.00[CEU][hapmap]
rs11695974	1.00[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs12474447	1.00[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs13021601	0.98[EUR][1000 genomes]
rs13025468	0.85[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs13422242	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34510112	0.82[EUR][1000 genomes]
rs4516428	1.00[CEU][hapmap]
rs6728112	0.83[EUR][1000 genomes]
rs6729910	0.85[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]
rs6757757	0.85[CEU][hapmap]
rs6759275	0.85[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs71414642	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7596661	1.00[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv874871	chr2:113021811-113217630	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv1801285	chr2:113113618-113200081	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs6542056	TTL	cis	parietal	SCAN
rs6542056	ZC3H8	cis	Artery Tibial	GTEx
rs6542056	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6542056	RGPD8	cis	Adipose Subcutaneous	GTEx
rs6542056	RGPD8	cis	Artery Aorta	GTEx
rs6542056	RGPD8	cis	Esophagus Muscularis	GTEx
rs6542056	RGPD8	cis	Esophagus Mucosa	GTEx
rs6542056	RGPD8	cis	Artery Tibial	GTEx
rs6542056	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs6542056	RGPD8	cis	Thyroid	GTEx
rs6542056	RGPD8	cis	Nerve Tibial	GTEx
rs6542056	RGPD8	cis	lung	GTEx
rs6542056	RGPD8	cis	Muscle Skeletal	GTEx
rs6542056	RGPD8	cis	Whole Blood	GTEx
rs6542056	RGPD8	cis	Heart Left Ventricle	GTEx
rs6542056	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113189600-113193000	Active TSS	HepG2	liver
2	chr2:113191000-113193000	Weak transcription	Spleen	Spleen
3	chr2:113191200-113192600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:113191200-113192600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:113191400-113192200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:113191400-113192200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:113191400-113192200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:113191400-113192200	Enhancers	Fetal Muscle Leg	muscle
9	chr2:113191400-113193200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:113191400-113194000	Enhancers	Placenta	Placenta
11	chr2:113191600-113192400	Enhancers	Fetal Brain Male	brain
12	chr2:113191800-113192200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:113191800-113192200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:113191800-113193000	Weak transcription	HMEC	breast
15	chr2:113192000-113192200	Bivalent Enhancer	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links