Variant report

Variant	rs4820845
Chromosome Location	chr22:30800338-30800339
allele	G/T
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	MYBL2	chr22:30800204-30800811	HepG2	liver:	n/a	n/a
2	SMC3	chr22:30800320-30800669	HepG2	liver:	n/a	n/a
3	POLR2A	chr22:30800257-30800632	HepG2	liver:	n/a	n/a
4	HNF4A	chr22:30800284-30800742	HepG2	liver:	n/a	chr22:30800450-30800465 chr22:30800452-30800460
5	SP1	chr22:30800314-30800782	HepG2	liver:	n/a	chr22:30800323-30800333
6	MAFK	chr22:30800319-30800673	HepG2	liver:	n/a	chr22:30800491-30800502 chr22:30800490-30800501 chr22:30800486-30800501 chr22:30800486-30800502 chr22:30800489-30800503 chr22:30800491-30800502
7	TEAD4	chr22:30800174-30800815	HepG2	liver:	n/a	n/a
8	MAFF	chr22:30800310-30800668	HepG2	liver:	n/a	n/a
9	POLR2A	chr22:30800134-30800504	K562	blood:	n/a	n/a
10	MAFK	chr22:30800305-30800686	HepG2	liver:	n/a	chr22:30800491-30800502 chr22:30800490-30800501 chr22:30800486-30800501 chr22:30800486-30800502 chr22:30800489-30800503 chr22:30800491-30800502
11	FOXA1	chr22:30800315-30800760	HepG2	liver:	n/a	n/a
12	HDAC2	chr22:30800213-30800729	HepG2	liver:	n/a	n/a
13	POLR2A	chr22:30800237-30800378	GM12878	blood:	n/a	n/a
14	HNF4G	chr22:30800242-30800736	HepG2	liver:	n/a	chr22:30800449-30800464 chr22:30800452-30800460
15	HNF4A	chr22:30800255-30800650	HepG2	liver:	n/a	chr22:30800450-30800465 chr22:30800452-30800460
16	FOXA1	chr22:30800338-30800751	HepG2	liver:	n/a	n/a
17	EP300	chr22:30800211-30800792	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30800239..30801947-chr22:30802123..30804894,2	K562	blood:
2	chr22:30792691..30796123-chr22:30800325..30803316,3	MCF-7	breast:

Variant related genes	Relation type
SEC14L2	TF binding region
ENSG00000249590	TF binding region
ENSG00000100003	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17658686	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2097919	0.81[CHD][hapmap]
rs2299824	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299829	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412985	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4820011	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753103	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs5753130	0.85[AFR][1000 genomes]
rs5763939	0.80[ASN][1000 genomes]
rs5994293	0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes]
rs5997602	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.80[ASN][1000 genomes]
rs7292432	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs737805	0.80[ASN][1000 genomes]
rs9608885	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4820845	CABP7	cis	cerebellum	SCAN
rs4820845	LIF	cis	cerebellum	SCAN
rs4820845	SF3A1	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30794000-30816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
3	chr22:30794400-30802200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:30794400-30811800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr22:30794600-30802200	Weak transcription	Aorta	Aorta
6	chr22:30794600-30803200	Weak transcription	Fetal Brain Male	brain
7	chr22:30794600-30803200	Weak transcription	Lung	lung
8	chr22:30794600-30811400	Weak transcription	Right Ventricle	heart
9	chr22:30794800-30802800	Weak transcription	Hela-S3	cervix
10	chr22:30794800-30811400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr22:30794800-30811600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr22:30794800-30818600	Weak transcription	Primary B cells from cord blood	blood
13	chr22:30795000-30802600	Weak transcription	Fetal Lung	lung
14	chr22:30795000-30809800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr22:30795000-30814600	Weak transcription	Colon Smooth Muscle	Colon
16	chr22:30795200-30801200	Weak transcription	Gastric	stomach
17	chr22:30795200-30801400	Weak transcription	Primary T cells from cord blood	blood
18	chr22:30795200-30801800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr22:30795200-30802200	Weak transcription	Fetal Brain Female	brain
20	chr22:30795200-30803000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr22:30795200-30804600	Weak transcription	NHDF-Ad	bronchial
22	chr22:30795200-30804800	Weak transcription	Pancreas	Pancrea
23	chr22:30795200-30807800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr22:30795200-30809000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr22:30795200-30810200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr22:30795200-30811600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr22:30795200-30814400	Weak transcription	Small Intestine	intestine
28	chr22:30795400-30802200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr22:30795400-30802400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr22:30795400-30803200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr22:30795400-30812000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr22:30795800-30802200	Weak transcription	Brain Germinal Matrix	brain
33	chr22:30796000-30801800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr22:30796000-30803200	Weak transcription	Spleen	Spleen
35	chr22:30796000-30813400	Weak transcription	Fetal Kidney	kidney
36	chr22:30796200-30804400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr22:30796200-30811400	Weak transcription	Placenta	Placenta
38	chr22:30796400-30802000	Weak transcription	Brain Anterior Caudate	brain
39	chr22:30796400-30803200	Weak transcription	Esophagus	oesophagus
40	chr22:30797000-30802400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr22:30797000-30804400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr22:30797200-30804600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr22:30797400-30803200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr22:30797600-30803200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr22:30797800-30803600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr22:30797800-30804600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr22:30797800-30805000	Genic enhancers	HMEC	breast
48	chr22:30797800-30816400	Strong transcription	Dnd41	blood
49	chr22:30798000-30800600	Enhancers	K562	blood
50	chr22:30798000-30804000	Strong transcription	NHEK	skin

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