Variant report

Variant	rs5753454
Chromosome Location	chr22:31475307-31475308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr22:31474875-31475414	HepG2	liver:	n/a	n/a
2	EP300	chr22:31475007-31475464	HepG2	liver:	n/a	chr22:31475173-31475183
3	HNF4A	chr22:31475020-31475487	HepG2	liver:	n/a	chr22:31475226-31475238 chr22:31475225-31475239 chr22:31475225-31475239 chr22:31475225-31475238 chr22:31475226-31475239 chr22:31475224-31475239 chr22:31475224-31475239 chr22:31475226-31475238
4	POLR2A	chr22:31475210-31475461	HepG2	liver:	n/a	n/a
5	MYC	chr22:31475193-31475432	HepG2	liver:	n/a	n/a
6	FOXA1	chr22:31474952-31475403	HepG2	liver:	n/a	n/a
7	FOXA1	chr22:31474948-31475412	HepG2	liver:	n/a	n/a
8	TEAD4	chr22:31475017-31475472	HepG2	liver:	n/a	n/a
9	RAD21	chr22:31475018-31475324	HepG2	liver:	n/a	n/a
10	FOXA1	chr22:31474869-31475435	HepG2	liver:	n/a	n/a
11	ZEB1	chr22:31474826-31475845	HepG2	liver:	n/a	chr22:31475405-31475416 chr22:31475404-31475416 chr22:31475406-31475413
12	SP2	chr22:31475168-31475679	HepG2	liver:	n/a	chr22:31475480-31475503
13	MBD4	chr22:31474963-31475685	HepG2	liver:	n/a	n/a
14	MYBL2	chr22:31474943-31475533	HepG2	liver:	n/a	n/a
15	TCF7L2	chr22:31475062-31475350	Hela-S3	cervix:	n/a	chr22:31475225-31475241 chr22:31475225-31475241 chr22:31475229-31475238 chr22:31475226-31475240 chr22:31475228-31475237 chr22:31475229-31475239
16	POLR2A	chr22:31475067-31475631	K562	blood:	n/a	n/a
17	EP300	chr22:31475053-31475409	HepG2	liver:	n/a	chr22:31475173-31475183
18	TCF7L2	chr22:31475126-31475452	HepG2	liver:	n/a	chr22:31475225-31475241 chr22:31475225-31475241 chr22:31475229-31475238 chr22:31475226-31475240 chr22:31475228-31475237 chr22:31475229-31475239
19	ZEB1	chr22:31474829-31475660	HepG2	liver:	n/a	chr22:31475405-31475416 chr22:31475404-31475416 chr22:31475406-31475413
20	BHLHE40	chr22:31475024-31475497	HepG2	liver:	n/a	n/a
21	POLR2A	chr22:31475011-31475518	HepG2	liver:	n/a	n/a
22	HEY1	chr22:31475108-31475562	HepG2	liver:	n/a	n/a
23	POLR2A	chr22:31474931-31476060	HepG2	liver:	n/a	n/a
24	MAX	chr22:31475143-31475448	HepG2	liver:	n/a	n/a
25	MYBL2	chr22:31474936-31475537	HepG2	liver:	n/a	n/a
26	POLR2A	chr22:31474941-31475539	HepG2	liver:	n/a	n/a
27	FOXA2	chr22:31474977-31475367	HepG2	liver:	n/a	n/a
28	HNF4A	chr22:31475058-31475338	HepG2	liver:	n/a	chr22:31475226-31475238 chr22:31475225-31475239 chr22:31475225-31475239 chr22:31475225-31475238 chr22:31475226-31475239 chr22:31475224-31475239 chr22:31475224-31475239 chr22:31475226-31475238
29	HNF4A	chr22:31475005-31475355	HepG2	liver:	n/a	chr22:31475226-31475238 chr22:31475225-31475239 chr22:31475225-31475239 chr22:31475225-31475238 chr22:31475226-31475239 chr22:31475224-31475239 chr22:31475224-31475239 chr22:31475226-31475238
30	NFIC	chr22:31474949-31475560	HepG2	liver:	n/a	n/a
31	HNF4G	chr22:31475002-31475553	HepG2	liver:	n/a	chr22:31475226-31475238 chr22:31475225-31475239 chr22:31475225-31475239 chr22:31475225-31475238 chr22:31475226-31475239 chr22:31475224-31475239 chr22:31475226-31475238
32	SP1	chr22:31474953-31475699	HepG2	liver:	n/a	n/a
33	RAD21	chr22:31475121-31475593	HepG2	liver:	n/a	n/a
34	POLR2A	chr22:31474992-31475582	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31360911..31371148-chr22:31475052..31483145,24	K562	blood:
2	chr22:31455769..31462183-chr22:31475245..31482356,13	K562	blood:
3	chr22:31358868..31372302-chr22:31474097..31485545,64	MCF-7	breast:
4	chr22:31475291..31477772-chr3:161087457..161089639,2	MCF-7	breast:
5	chr22:31457775..31462699-chr22:31474304..31478789,5	MCF-7	breast:

Variant related genes	Relation type
SMTN	TF binding region
ENSG00000196542	Chromatin interaction
ENSG00000253352	Chromatin interaction
ENSG00000133422	Chromatin interaction
ENSG00000183963	Chromatin interaction
ENSG00000240186	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10304	0.91[CHB][hapmap]
rs12484162	1.00[ASW][hapmap]
rs12484314	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2267167	0.91[CHB][hapmap]
rs2283875	0.91[CHB][hapmap]
rs2283877	0.91[CHB][hapmap]
rs4820942	0.86[CHB][hapmap]
rs5753466	0.91[CHB][hapmap]
rs5997867	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8140524	0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs9606811	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv914975	chr22:31466083-31514477	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv979668	chr22:31473892-31475436	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv914976	chr22:31475307-31543260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5753454	SFI1	cis	cerebellum	SCAN
rs5753454	CRYBA4	cis	cerebellum	SCAN
rs5753454	RNF185	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31469800-31476400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr22:31469800-31476400	Weak transcription	HUVEC	blood vessel
3	chr22:31471400-31476600	Weak transcription	Left Ventricle	heart
4	chr22:31472000-31476400	Weak transcription	HSMMtube	muscle
5	chr22:31472200-31475400	Weak transcription	Lung	lung
6	chr22:31472200-31476200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr22:31472200-31476400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr22:31472400-31476400	Weak transcription	Ovary	ovary
9	chr22:31472400-31476600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr22:31472400-31476600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr22:31472400-31476600	Weak transcription	Psoas Muscle	Psoas
12	chr22:31472600-31476200	Weak transcription	Fetal Lung	lung
13	chr22:31472600-31476400	Weak transcription	Adipose Nuclei	Adipose
14	chr22:31472600-31476400	Weak transcription	Right Ventricle	heart
15	chr22:31472600-31476400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr22:31472600-31476400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr22:31472600-31476400	Weak transcription	NHDF-Ad	bronchial
18	chr22:31472600-31476600	Weak transcription	Right Atrium	heart
19	chr22:31472600-31476600	Weak transcription	NHLF	lung
20	chr22:31473600-31476400	Enhancers	Fetal Intestine Large	intestine
21	chr22:31473800-31475400	Enhancers	Placenta	Placenta
22	chr22:31473800-31476400	Enhancers	Fetal Intestine Small	intestine
23	chr22:31473800-31476400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr22:31474200-31475400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr22:31474200-31476400	Enhancers	Fetal Muscle Leg	muscle
26	chr22:31474200-31476600	Enhancers	Fetal Stomach	stomach
27	chr22:31474400-31475400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr22:31474400-31475600	Enhancers	Stomach Mucosa	stomach
29	chr22:31474600-31476400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:31474600-31476400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr22:31474600-31476400	Weak transcription	HMEC	breast
32	chr22:31474600-31476400	Weak transcription	HSMM	muscle
33	chr22:31474600-31476600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr22:31474600-31476600	Weak transcription	Esophagus	oesophagus
35	chr22:31474600-31476600	Weak transcription	Osteobl	bone
36	chr22:31474800-31475800	Flanking Active TSS	HepG2	liver
37	chr22:31474800-31476400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr22:31474800-31476400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr22:31474800-31476400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr22:31475000-31475400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr22:31475000-31475400	Enhancers	Gastric	stomach
42	chr22:31475000-31475400	Enhancers	Spleen	Spleen
43	chr22:31475000-31475600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr22:31475000-31475800	Enhancers	H9 Cell Line	embryonic stem cell
45	chr22:31475000-31475800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr22:31475000-31475800	Enhancers	Colonic Mucosa	Colon
47	chr22:31475000-31475800	Enhancers	Fetal Muscle Trunk	muscle
48	chr22:31475000-31476400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr22:31475000-31476400	Weak transcription	NHEK	skin
50	chr22:31475000-31476600	Weak transcription	Brain Germinal Matrix	brain

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