Variant report

Variant	rs13033042
Chromosome Location	chr2:55195220-55195221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55195018-55195402	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:55194876-55196816	HL-60	blood:	n/a	n/a
3	POLR2A	chr2:55194954-55195501	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr2:55193058-55197604	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr2:55194430-55195407	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr2:55192057-55196307	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr2:55193400-55197464	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr2:55194897-55195386	A549	lung:	n/a	n/a
9	POLR2A	chr2:55193200-55198888	A549	lung:	n/a	n/a
10	POLR2A	chr2:55190471-55199022	SK-N-SH	brain:	n/a	n/a
11	SIN3AK20	chr2:55194624-55195229	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr2:55193167-55197152	U87	brain:	n/a	n/a
13	POLR2A	chr2:55195083-55196179	GM19193	blood:	n/a	n/a
14	POLR2A	chr2:55194740-55195290	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:55194909-55196368	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr2:55194875-55196815	HCT-116	colon:	n/a	n/a
17	POLR2A	chr2:55190362-55199062	U87	brain:	n/a	n/a
18	POLR2A	chr2:55194668-55195383	MCF-7	breast:	n/a	n/a
19	POLR2A	chr2:55194189-55195244	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr2:55194892-55195302	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:55194821-55197414	GM12891	blood:	n/a	n/a
22	POLR2A	chr2:55194952-55195390	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:55194819-55195966	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr2:55195043-55196265	K562	blood:	n/a	n/a
25	POLR2A	chr2:55193167-55197203	U87	brain:	n/a	n/a
26	POLR2A	chr2:55194919-55195347	ProgFib	skin:	n/a	n/a
27	POLR2A	chr2:55194328-55196339	HL-60	blood:	n/a	n/a
28	POLR2A	chr2:55193277-55201440	K562	blood:	n/a	n/a
29	POLR2A	chr2:55195057-55196274	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr2:55194719-55195464	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr2:55191336-55197109	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr2:55194497-55197512	K562	blood:	n/a	n/a
33	FOSL2	chr2:55195108-55196306	HepG2	liver:	n/a	n/a
34	POLR2A	chr2:55195159-55195235	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr2:55194675-55195492	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr2:55193180-55198666	IMR90	lung:	n/a	n/a
37	POLR2A	chr2:55194841-55195385	K562	blood:	n/a	n/a
38	POLR2A	chr2:55194960-55195396	A549	lung:	n/a	n/a
39	POLR2A	chr2:55194734-55195754	HUVEC	blood vessel:	n/a	n/a
40	USF2	chr2:55195138-55195285	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr2:55190362-55199105	U87	brain:	n/a	n/a

No data

Variant related genes	Relation type
EML6	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1012603	1.00[YRI][hapmap]
rs10496038	1.00[MEX][hapmap]
rs11677099	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11684017	0.84[EUR][1000 genomes]
rs11686912	1.00[MEX][hapmap]
rs11696046	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs11894868	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs13021245	0.85[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs13027633	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13030462	0.85[CHB][hapmap]
rs6742306	1.00[MEX][hapmap]
rs7595814	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13033042	SPTBN1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55173200-55203400	Weak transcription	Gastric	stomach
2	chr2:55180600-55195400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr2:55180600-55196000	Weak transcription	NH-A	brain
4	chr2:55181600-55203400	Weak transcription	Ovary	ovary
5	chr2:55183200-55206800	Weak transcription	Stomach Mucosa	stomach
6	chr2:55183400-55196600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:55184800-55195800	Weak transcription	Thymus	Thymus
8	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:55190000-55198400	Weak transcription	Colonic Mucosa	Colon
10	chr2:55190000-55203400	Weak transcription	Small Intestine	intestine
11	chr2:55190600-55198000	Genic enhancers	Fetal Muscle Leg	muscle
12	chr2:55190800-55196600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:55191200-55195400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:55191200-55198200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:55191200-55199200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:55191400-55195400	Weak transcription	Fetal Intestine Large	intestine
17	chr2:55191800-55203600	Weak transcription	Fetal Lung	lung
18	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:55192200-55198600	Strong transcription	Fetal Stomach	stomach
21	chr2:55192600-55195400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr2:55192600-55195400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:55192600-55198600	Strong transcription	Fetal Intestine Small	intestine
24	chr2:55193200-55195400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:55193400-55196200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:55193400-55196200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:55193400-55196800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr2:55193400-55197400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:55193400-55199000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:55193400-55201800	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr2:55193400-55214800	Strong transcription	HepG2	liver
32	chr2:55193600-55195800	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:55193600-55196400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:55193600-55196400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:55193600-55197000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:55193600-55197400	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr2:55193600-55200800	Strong transcription	A549	lung
38	chr2:55193600-55201800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:55193800-55195600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:55193800-55196800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:55193800-55197400	Enhancers	Psoas Muscle	Psoas
43	chr2:55193800-55198200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:55193800-55198600	Genic enhancers	Lung	lung
45	chr2:55193800-55202400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:55194000-55198600	Strong transcription	Brain Germinal Matrix	brain
48	chr2:55194000-55199000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:55194200-55195400	Weak transcription	Esophagus	oesophagus

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