Variant report

Variant	rs554202
Chromosome Location	chr11:75428958-75428959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:75428910-75428960	HNPCEpiC	eye:	n/a
2	chr11:75428910-75428960	MCF10A-Er-Src	breast:	n/a
3	chr11:75428910-75428960	HPAEpiC	pulmonary alveolar:	n/a
4	chr11:75428910-75428960	MCF-7	breast:	n/a
5	chr11:75428927-75428977	HAEpiC	amniotic membrane:	n/a
6	chr11:75428927-75428977	SK-N-SH_RA	brain:	n/a
7	chr11:75428927-75428977	PrEC	prostate:	n/a
8	chr11:75428927-75428977	Caco-2	colon:	n/a
9	chr11:75428910-75428960	HCT-116	colon:	n/a
10	chr11:75428910-75428960	PFSK-1	brain:	n/a
11	chr11:75428910-75428960	HCPEpiC	choroid plexus:	n/a
12	chr11:75428927-75428977	RPTEC	kidney:	n/a
13	chr11:75428910-75428960	HCM	heart:	n/a
14	chr11:75428910-75428960	SK-N-MC	brain:	n/a
15	chr11:75428927-75428977	AG09309	skin:	n/a
16	chr11:75428910-75428960	NT2-D1	testis:	n/a
17	chr11:75428910-75428960	A549	lung:	n/a
18	chr11:75428910-75428960	HAEpiC	amniotic membrane:	n/a
19	chr11:75428927-75428977	LNCaP	prostate:	n/a
20	chr11:75428927-75428977	HCT-116	colon:	n/a
21	chr11:75428927-75428977	NHDF-neo	bronchial:	n/a
22	chr11:75428927-75428977	IMR90	lung:	fetal
23	chr11:75428927-75428977	HIPEpiC	eye:	n/a
24	chr11:75428927-75428977	A549	lung:	n/a
25	chr11:75428910-75428960	AG04450	lung:	fetal
26	chr11:75428927-75428977	HUVEC	blood vessel:	n/a
27	chr11:75428927-75428977	H1-hESC	embryonic stem cell:	embryo
28	chr11:75428927-75428977	CMK	blood:	n/a
29	chr11:75428910-75428960	HUVEC	blood vessel:	n/a
30	chr11:75428927-75428977	SK-N-SH	brain:	n/a
31	chr11:75428927-75428977	HL-60	blood:	n/a
32	chr11:75428910-75428960	HMEC	breast:	n/a
33	chr11:75428910-75428960	BJ	skin:	n/a
34	chr11:75428910-75428960	AG10803	skin:	n/a
35	chr11:75428927-75428977	HNPCEpiC	eye:	n/a
36	chr11:75428910-75428960	SK-N-SH_RA	brain:	n/a
37	chr11:75428927-75428977	MCF10A-Er-Src	breast:	n/a
38	chr11:75428910-75428960	NB4	blood:	n/a
39	chr11:75428927-75428977	BJ	skin:	n/a
40	chr11:75428927-75428977	HRCEpiC	kidney:	n/a
41	chr11:75428927-75428977	GM06990	blood:	n/a
42	chr11:75428927-75428977	Hepatocyte	liver:	n/a
43	chr11:75428927-75428977	NH-A	brain:	n/a
44	chr11:75428927-75428977	AG09319	gingival:	n/a
45	chr11:75428910-75428960	Jurkat	blood:	n/a
46	chr11:75428910-75428960	NHBE	bronchial:	n/a
47	chr11:75428910-75428960	BE2_C	brain:	n/a
48	chr11:75428927-75428977	GM19239	blood:	n/a
49	chr11:75428927-75428977	MCF-7	breast:	n/a
50	chr11:75428927-75428977	GM12892	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:75273373..75275096-chr11:75428137..75429945,2	MCF-7	breast:

No data

Variant related genes	Relation type
MOGAT2	CpG island
ENSG00000149257	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10793123	0.81[EUR][1000 genomes]
rs10899102	0.89[EUR][1000 genomes]
rs1145700	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1219536	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs1219537	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1219538	1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1219539	0.88[EUR][1000 genomes]
rs1238914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473013	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs473791	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs623693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650861	1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv897924	chr11:75424546-75678647	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs554202	PFAS	cis	Liver	GTEx
rs554202	GAB2	cis	parietal	SCAN
rs554202	MRPL11	trans	multi-tissue	Pritchard
rs554202	LRRC32	cis	parietal	SCAN
rs554202	PFAS	trans	multi-tissue	Pritchard
rs554202	RPS3	cis	multi-tissue	Pritchard
rs554202	hCT18544.2	cis	multi-tissue	Pritchard
rs554202	NUMA1	cis	parietal	SCAN
rs554202	MRPL11	cis	Liver	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75427200-75429400	Enhancers	HepG2	liver
2	chr11:75427600-75429000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:75428000-75429600	Enhancers	Liver	Liver
4	chr11:75428200-75429000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr11:75428200-75431200	Enhancers	Gastric	stomach
6	chr11:75428400-75429400	Active TSS	Colonic Mucosa	Colon
7	chr11:75428600-75429000	Active TSS	Fetal Intestine Large	intestine
8	chr11:75428600-75429000	Flanking Active TSS	Fetal Intestine Small	intestine
9	chr11:75428600-75429000	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr11:75428600-75429200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:75428600-75430200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:75428600-75430600	Active TSS	Duodenum Mucosa	Duodenum
13	chr11:75428600-75431000	Enhancers	Stomach Mucosa	stomach
14	chr11:75428800-75429000	Enhancers	Spleen	Spleen
15	chr11:75428800-75429000	Enhancers	HMEC	breast
16	chr11:75428800-75429200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:75428800-75429200	Enhancers	Esophagus	oesophagus
18	chr11:75428800-75429600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:75428800-75429600	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr11:75428800-75430000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr11:75428800-75430200	Enhancers	Right Ventricle	heart
22	chr11:75428800-75430400	Enhancers	Adipose Nuclei	Adipose
23	chr11:75428800-75431000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr11:75428800-75431000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr11:75428800-75431200	Enhancers	Left Ventricle	heart
26	chr11:75428800-75431200	Active TSS	Rectal Smooth Muscle	rectum

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