Variant report

Variant	rs2283870
Chromosome Location	chr22:30800312-30800313
allele	C/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	POLR2A	chr22:30800257-30800632	HepG2	liver:	n/a	n/a
3	HNF4A	chr22:30800284-30800742	HepG2	liver:	n/a	chr22:30800450-30800465 chr22:30800452-30800460
4	TEAD4	chr22:30800174-30800815	HepG2	liver:	n/a	n/a
5	MAFF	chr22:30800310-30800668	HepG2	liver:	n/a	n/a
6	POLR2A	chr22:30800134-30800504	K562	blood:	n/a	n/a
7	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
8	HDAC2	chr22:30800213-30800729	HepG2	liver:	n/a	n/a
9	POLR2A	chr22:30800237-30800378	GM12878	blood:	n/a	n/a
10	HNF4G	chr22:30800242-30800736	HepG2	liver:	n/a	chr22:30800449-30800464 chr22:30800452-30800460
11	HNF4A	chr22:30800255-30800650	HepG2	liver:	n/a	chr22:30800450-30800465 chr22:30800452-30800460
12	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:

Variant related genes	Relation type
SEC14L2	TF binding region
ENSG00000249590	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1005835	0.84[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs1010324	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11089442	0.82[CEU][hapmap]
rs11089447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11089448	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11089449	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11703867	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11705639	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12171261	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2072160	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2074731	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2267154	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267155	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267156	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283866	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2283871	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299827	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2839998	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57940170	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5994294	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5994305	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5994306	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5997637	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5997646	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61583714	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71331235	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7288366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7289360	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7290317	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8141656	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9619096	0.91[CEU][hapmap]
rs9619098	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9619105	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9620984	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No data

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links