Variant report

Variant	rs5753071
Chromosome Location	chr22:30726826-30726827
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:30726436-30727033	GM12891	blood:	n/a	n/a
2	POLR2A	chr22:30726679-30726975	A549	lung:	n/a	n/a
3	POLR2A	chr22:30726458-30727566	GM12892	blood:	n/a	n/a
4	POLR2A	chr22:30726458-30727203	GM12891	blood:	n/a	n/a
5	GATA3	chr22:30726723-30727294	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr22:30726700-30727141	HepG2	liver:	n/a	n/a
7	POLR2A	chr22:30726477-30727103	GM12892	blood:	n/a	n/a
8	POLR2A	chr22:30726482-30727220	GM12878	blood:	n/a	n/a
9	POLR2A	chr22:30726688-30727130	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr22:30726780-30727049	H1-hESC	embryonic stem cell:	n/a	n/a
11	EP300	chr22:30726683-30727050	T-47D	breast:	n/a	n/a
12	POLR2A	chr22:30726614-30727111	GM12892	blood:	n/a	n/a
13	GATA3	chr22:30726685-30727164	MCF-7	breast:	n/a	n/a
14	POLR2A	chr22:30726557-30727023	GM12878	blood:	n/a	n/a
15	GATA3	chr22:30726805-30727106	T-47D	breast:	n/a	n/a
16	GATA3	chr22:30726708-30727164	T-47D	breast:	n/a	n/a
17	POLR2A	chr22:30726815-30726923	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr22:30726690-30727170	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr22:30726516-30727578	K562	blood:	n/a	n/a
20	POLR2A	chr22:30726779-30727103	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr22:30726637-30727011	K562	blood:	n/a	n/a
22	POLR2A	chr22:30726495-30727119	GM12892	blood:	n/a	n/a
23	POLR2A	chr22:30726470-30727197	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr22:30726579-30727163	MCF-7	breast:	n/a	n/a
25	GATA3	chr22:30726697-30727392	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30679955..30682000-chr22:30725118..30726971,2	K562	blood:
2	chr22:30723840..30727994-chr22:30728827..30733130,4	K562	blood:
3	chr22:30720496..30722809-chr22:30723809..30726893,3	MCF-7	breast:
4	chr22:30723090..30724854-chr22:30725952..30728416,2	K562	blood:
5	chr22:30726026..30729085-chr22:30749869..30754191,5	MCF-7	breast:
6	chr22:30710168..30712716-chr22:30726036..30728244,2	MCF-7	breast:
7	chr22:30679226..30682000-chr22:30723679..30728534,4	K562	blood:

No data

Variant related genes	Relation type
TBC1D10A	TF binding region
ENSG00000099995	Chromatin interaction
ENSG00000187860	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427610	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043099	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041199	0.89[AMR][1000 genomes]
rs2108093	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299830	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4339043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820831	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4820844	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4823085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5749066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749082	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5753080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753088	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753111	1.00[ASN][1000 genomes]
rs5763923	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs737950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs740219	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757869	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs929454	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608904	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9619104	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv984527	chr22:30698358-30732712	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv3593	chr22:30705980-30751122	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
6	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
7	nsv1064350	chr22:30724148-30742125	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	n/a
8	nsv1066179	chr22:30724148-30766466	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5753071	SF3A1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30723000-30728400	Weak transcription	Small Intestine	intestine
2	chr22:30723400-30727400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:30723400-30728400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr22:30723400-30728600	Weak transcription	Esophagus	oesophagus
5	chr22:30723400-30728600	Weak transcription	Right Ventricle	heart
6	chr22:30723400-30728800	Weak transcription	Ovary	ovary
7	chr22:30723400-30729400	Weak transcription	Psoas Muscle	Psoas
8	chr22:30723400-30732600	Weak transcription	Right Atrium	heart
9	chr22:30723600-30728200	Weak transcription	NHLF	lung
10	chr22:30723600-30728400	Weak transcription	Brain Hippocampus Middle	brain
11	chr22:30723600-30728400	Weak transcription	Colon Smooth Muscle	Colon
12	chr22:30723600-30728600	Weak transcription	Aorta	Aorta
13	chr22:30723600-30729400	Weak transcription	Fetal Brain Male	brain
14	chr22:30723600-30730400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr22:30723600-30751600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr22:30723800-30727000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr22:30723800-30727200	Weak transcription	HUVEC	blood vessel
18	chr22:30723800-30728400	Weak transcription	Brain Angular Gyrus	brain
19	chr22:30723800-30729200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr22:30723800-30742800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr22:30724000-30728200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr22:30724000-30728600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr22:30724000-30728600	Weak transcription	Pancreas	Pancrea
24	chr22:30724000-30729200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr22:30724200-30728400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr22:30724200-30728400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr22:30724200-30728400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr22:30724200-30731200	Weak transcription	Hela-S3	cervix
29	chr22:30724400-30727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr22:30724400-30728400	Weak transcription	HMEC	breast
31	chr22:30724400-30729200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr22:30724400-30750000	Strong transcription	Thymus	Thymus
33	chr22:30724600-30728400	Weak transcription	HepG2	liver
34	chr22:30724600-30729400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr22:30724600-30750200	Strong transcription	Osteobl	bone
36	chr22:30724800-30728600	Weak transcription	Stomach Mucosa	stomach
37	chr22:30724800-30745200	Strong transcription	NHEK	skin
38	chr22:30724800-30750200	Strong transcription	Fetal Intestine Small	intestine
39	chr22:30725000-30729400	Weak transcription	Fetal Heart	heart
40	chr22:30725200-30733200	Strong transcription	Fetal Muscle Leg	muscle
41	chr22:30725400-30733400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr22:30725400-30743400	Strong transcription	Fetal Stomach	stomach
43	chr22:30725400-30749600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr22:30725400-30750000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr22:30725600-30727600	Strong transcription	Colonic Mucosa	Colon
46	chr22:30725600-30729400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr22:30725600-30733600	Genic enhancers	Placenta	Placenta
48	chr22:30725600-30743600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr22:30725600-30744200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr22:30725600-30750200	Strong transcription	Fetal Intestine Large	intestine

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