Variant report

Variant	rs4820844
Chromosome Location	chr22:30795215-30795216
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	GATA1	chr22:30794816-30795324	PBDE	blood:	n/a	chr22:30795115-30795125
2	POLR2A	chr22:30793321-30795253	Raji	blood:	n/a	n/a
3	MAX	chr22:30794885-30795260	NB4	blood:	n/a	n/a
4	POLR2A	chr22:30793524-30795326	PBDE	blood:	n/a	n/a
5	POLR2A	chr22:30791787-30796585	GM12878	blood:	n/a	n/a
6	POLR2A	chr22:30792617-30795297	GM12878	blood:	n/a	n/a
7	POLR2A	chr22:30792819-30795221	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr22:30795044-30795263	K562	blood:	n/a	n/a
9	POLR2A	chr22:30794846-30795316	HL-60	blood:	n/a	n/a
10	POLR2A	chr22:30793918-30795516	HepG2	liver:	n/a	n/a
11	POLR2A	chr22:30794473-30795298	GM12878	blood:	n/a	n/a
12	POLR2A	chr22:30792640-30795327	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30787731..30797808-chr22:30813672..30825727,31	MCF-7	breast:
2	chr22:30791754..30798377-chr22:30814746..30822334,13	K562	blood:

Variant related genes	Relation type
SEC14L2	TF binding region
ENSG00000268538	Chromatin interaction
ENSG00000273350	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000222915	Chromatin interaction
ENSG00000272689	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1009337	0.85[MEX][hapmap]
rs10376	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs10427610	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1043099	0.82[ASN][1000 genomes]
rs1046199	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap]
rs2108093	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2299830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4339043	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4820008	0.82[ASN][1000 genomes]
rs4820831	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4820846	0.87[EUR][1000 genomes]
rs4820847	0.87[EUR][1000 genomes]
rs4823085	0.80[ASN][1000 genomes]
rs5749066	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs5749078	0.82[ASN][1000 genomes]
rs5749082	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753071	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs5753080	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs5753111	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753124	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5763923	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs5997642	0.84[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs7284527	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs737723	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs737950	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs740219	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs757869	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs929454	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9608904	1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9619104	0.82[ASN][1000 genomes]
rs9620979	0.82[AMR][1000 genomes];0.86[EUR][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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4820844	PAIP2B	trans	cerebellum	SCAN
rs4820844	SF3A1	cis	multi-tissue	Pritchard
rs4820844	OR4N5	trans	cerebellum	SCAN
rs4820844	ZNF284	trans	parietal	SCAN
rs4820844	RFPL2	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30792600-30795400	Enhancers	Spleen	Spleen
2	chr22:30792800-30795600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:30793400-30795400	Flanking Active TSS	Dnd41	blood
4	chr22:30793600-30795400	Flanking Active TSS	Liver	Liver
5	chr22:30793600-30795400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
6	chr22:30793800-30795400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr22:30794000-30816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
9	chr22:30794200-30795800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr22:30794200-30796200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr22:30794200-30797800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr22:30794200-30797800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr22:30794400-30802200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:30794400-30811800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr22:30794600-30795400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr22:30794600-30795400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr22:30794600-30795400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr22:30794600-30796200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr22:30794600-30796400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr22:30794600-30798000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr22:30794600-30798000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr22:30794600-30802200	Weak transcription	Aorta	Aorta
23	chr22:30794600-30803200	Weak transcription	Fetal Brain Male	brain
24	chr22:30794600-30803200	Weak transcription	Lung	lung
25	chr22:30794600-30811400	Weak transcription	Right Ventricle	heart
26	chr22:30794800-30795800	Enhancers	Brain Germinal Matrix	brain
27	chr22:30794800-30796200	Enhancers	HepG2	liver
28	chr22:30794800-30796400	Enhancers	Stomach Smooth Muscle	stomach
29	chr22:30794800-30796600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
30	chr22:30794800-30796600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr22:30794800-30796600	Enhancers	Fetal Thymus	thymus
32	chr22:30794800-30797800	Weak transcription	A549	lung
33	chr22:30794800-30798000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr22:30794800-30802800	Weak transcription	Hela-S3	cervix
35	chr22:30794800-30811400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr22:30794800-30811600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr22:30794800-30818600	Weak transcription	Primary B cells from cord blood	blood
38	chr22:30795000-30795400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr22:30795000-30795400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr22:30795000-30795400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr22:30795000-30795400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr22:30795000-30795400	Active TSS	Brain Anterior Caudate	brain
43	chr22:30795000-30795800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr22:30795000-30796000	Active TSS	Brain Substantia Nigra	brain
45	chr22:30795000-30796400	Enhancers	Brain Hippocampus Middle	brain
46	chr22:30795000-30802600	Weak transcription	Fetal Lung	lung
47	chr22:30795000-30809800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr22:30795000-30814600	Weak transcription	Colon Smooth Muscle	Colon
49	chr22:30795200-30795400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr22:30795200-30795400	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links