Variant report

Variant	rs2645339
Chromosome Location	chr5:178416063-178416064
allele	C/T
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:1)
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	chr5:178416050-178416100	ProgFib	skin:	n/a
2	chr5:178416050-178416100	NH-A	brain:	n/a
3	chr5:178416050-178416100	SK-N-MC	brain:	n/a
4	chr5:178416050-178416100	Hela-S3	cervix:	n/a
5	chr5:178416050-178416100	ovcar-3	ovarian:	n/a
6	chr5:178416050-178416100	BJ	skin:	n/a
7	chr5:178416050-178416100	AG10803	skin:	n/a
8	chr5:178416050-178416100	HRCEpiC	kidney:	n/a
9	chr5:178416050-178416100	K562	blood:	n/a
10	chr5:178416050-178416100	PANC-1	pancreas:	n/a
11	chr5:178416050-178416100	HCT-116	colon:	n/a
12	chr5:178416050-178416100	MCF-7	breast:	n/a
13	chr5:178416050-178416100	GM06990	blood:	n/a
14	chr5:178416050-178416100	ECC-1	luminal epithelium:	n/a
15	chr5:178416050-178416100	GM12891	blood:	n/a
16	chr5:178416050-178416100	AoSMC	blood vessel:	n/a
17	chr5:178416050-178416100	HMEC	breast:	n/a
18	chr5:178416050-178416100	NB4	blood:	n/a
19	chr5:178416050-178416100	H1-hESC	embryonic stem cell:	embryo
20	chr5:178416050-178416100	PrEC	prostate:	n/a
21	chr5:178416050-178416100	AG09319	gingival:	n/a
22	chr5:178416050-178416100	AG09309	skin:	n/a
23	chr5:178416050-178416100	RPTEC	kidney:	n/a
24	chr5:178416050-178416100	LNCaP	prostate:	n/a
25	chr5:178416050-178416100	HIPEpiC	eye:	n/a
26	chr5:178416050-178416100	T-47D	breast:	n/a
27	chr5:178416050-178416100	Hepatocyte	liver:	n/a
28	chr5:178416050-178416100	HRE	kidney:	n/a
29	chr5:178416050-178416100	HL-60	blood:	n/a
30	chr5:178416050-178416100	HAEpiC	amniotic membrane:	n/a
31	chr5:178416050-178416100	MCF10A-Er-Src	breast:	n/a
32	chr5:178416050-178416100	CMK	blood:	n/a
33	chr5:178416050-178416100	GM12892	blood:	n/a
34	chr5:178416050-178416100	AG04450	lung:	fetal
35	chr5:178416050-178416100	HPAEpiC	pulmonary alveolar:	n/a
36	chr5:178416050-178416100	HCF	heart:	n/a
37	chr5:178416050-178416100	HRPEpiC	eye:	n/a
38	chr5:178416050-178416100	HepG2	liver:	n/a
39	chr5:178416050-178416100	BE2_C	brain:	n/a
40	chr5:178416050-178416100	HCM	heart:	n/a
41	chr5:178416050-178416100	SKMC	muscle:	n/a
42	chr5:178416050-178416100	GM19239	blood:	n/a
43	chr5:178416050-178416100	HNPCEpiC	eye:	n/a
44	chr5:178416050-178416100	Caco-2	colon:	n/a
45	chr5:178416050-178416100	SK-N-SH	brain:	n/a
46	chr5:178416050-178416100	HUVEC	blood vessel:	n/a
47	chr5:178416050-178416100	HEEpiC	esophagus:	n/a
48	chr5:178416050-178416100	U87	brain:	n/a
49	chr5:178416050-178416100	AG04449	skin:	fetal
50	chr5:178416050-178416100	HEK293	kidney:	embryo

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178415802..178417624-chr5:178422494..178424100,2	MCF-7	breast:

No data

Variant related genes	Relation type
GRM6	CpG island
ENSG00000113262	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11746675	0.94[ASW][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs2067011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071246	0.87[JPT][hapmap]
rs2256966	0.94[ASW][hapmap];0.81[CHB][hapmap];0.95[LWK][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2645329	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2645330	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6600998	0.92[EUR][1000 genomes]
rs762724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs762725	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600489	chr5:178368096-178430375	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1017941	chr5:178384214-178427401	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv537974	chr5:178384214-178427401	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv883219	chr5:178390237-178454118	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv883220	chr5:178394717-178454118	ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv600490	chr5:178405251-178430375	Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv883221	chr5:178410538-178454118	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2645339	MGAT1	cis	cerebellum	SCAN
rs2645339	RNF44	cis	cerebellum	SCAN
rs2645339	ZNF879	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178369400-178418200	ZNF genes & repeats	Fetal Brain Female	brain
2	chr5:178405400-178418200	ZNF genes & repeats	Brain Germinal Matrix	brain
3	chr5:178413000-178417400	ZNF genes & repeats	Fetal Stomach	stomach
4	chr5:178413200-178417200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
5	chr5:178415800-178417800	ZNF genes & repeats	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links