Variant report

Variant	rs13306260
Chromosome Location	chr2:189867239-189867240
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	FOSL2	chr2:189866721-189867284	SK-N-SH	brain:	n/a	n/a
2	JUND	chr2:189866636-189867352	SK-N-SH	brain:	n/a	n/a
3	SP1	chr2:189866676-189867289	HCT-116	colon:	n/a	n/a
4	JUND	chr2:189866737-189867251	HCT-116	colon:	n/a	n/a
5	JUND	chr2:189866764-189867346	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr2:189866060-189867376	SK-N-SH	brain:	n/a	chr2:189866938-189866947 chr2:189866958-189866968 chr2:189866940-189866947 chr2:189866940-189866947 chr2:189866933-189866954 chr2:189866939-189866947 chr2:189866943-189866959 chr2:189866915-189866925 chr2:189866940-189866947
7	TEAD4	chr2:189866707-189867263	SK-N-SH	brain:	n/a	n/a
8	EP300	chr2:189866712-189867376	SK-N-SH	brain:	n/a	chr2:189866917-189866926
9	SP1	chr2:189866756-189867320	HCT-116	colon:	n/a	n/a
10	GATA3	chr2:189866548-189867377	SK-N-SH	brain:	n/a	chr2:189866938-189866947 chr2:189866958-189866968 chr2:189866940-189866947 chr2:189866940-189866947 chr2:189866933-189866954 chr2:189866939-189866947 chr2:189866943-189866959 chr2:189866915-189866925 chr2:189866940-189866947
11	TCF12	chr2:189866595-189867412	SK-N-SH	brain:	n/a	n/a
12	JUND	chr2:189866766-189867385	SK-N-SH	brain:	n/a	n/a
13	CBX3	chr2:189866750-189867300	HCT-116	colon:	n/a	n/a
14	CHD1	chr2:189866740-189867368	IMR90	lung:	n/a	n/a
15	EP300	chr2:189866555-189867430	SK-N-SH	brain:	n/a	chr2:189866917-189866926
16	PBX3	chr2:189866776-189867255	SK-N-SH	brain:	n/a	n/a
17	MAX	chr2:189866710-189867283	A549	lung:	n/a	n/a
18	GATA3	chr2:189866755-189867305	MCF-7	breast:	n/a	chr2:189866938-189866947 chr2:189866958-189866968 chr2:189866940-189866947 chr2:189866940-189866947 chr2:189866933-189866954 chr2:189866939-189866947 chr2:189866943-189866959 chr2:189866915-189866925 chr2:189866940-189866947
19	TCF12	chr2:189866601-189867289	A549	lung:	n/a	n/a
20	POLR2A	chr2:189866735-189869543	SK-N-SH	brain:	n/a	n/a
21	NR2F2	chr2:189866823-189867309	MCF-7	breast:	n/a	n/a
22	NFIC	chr2:189866689-189867345	SK-N-SH	brain:	n/a	n/a
23	GATA3	chr2:189866540-189867343	A549	lung:	n/a	chr2:189866938-189866947 chr2:189866958-189866968 chr2:189866940-189866947 chr2:189866940-189866947 chr2:189866933-189866954 chr2:189866939-189866947 chr2:189866943-189866959 chr2:189866915-189866925 chr2:189866940-189866947
24	TCF12	chr2:189866599-189867345	SK-N-SH	brain:	n/a	n/a
25	FOSL2	chr2:189866726-189867254	A549	lung:	n/a	n/a
26	MAX	chr2:189866798-189867239	SK-N-SH	brain:	n/a	n/a
27	PBX3	chr2:189866763-189867303	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189866664..189868828-chr2:189872499..189874022,2	MCF-7	breast:

Variant related genes	Relation type
COL3A1	TF binding region
ENSG00000168542	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10191859	1.00[EUR][1000 genomes]
rs10201930	1.00[EUR][1000 genomes]
rs10497695	0.87[ASN][1000 genomes]
rs10497696	1.00[EUR][1000 genomes]
rs11902058	0.87[ASN][1000 genomes]
rs12105286	0.89[ASN][1000 genomes]
rs12105340	0.89[ASN][1000 genomes]
rs12619321	0.94[ASN][1000 genomes]
rs13306257	0.89[ASN][1000 genomes]
rs13306267	0.87[ASN][1000 genomes]
rs13306268	0.87[ASN][1000 genomes]
rs13306269	0.87[ASN][1000 genomes]
rs13425379	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16830965	0.92[ASN][1000 genomes]
rs16830983	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16830984	1.00[EUR][1000 genomes]
rs2271679	0.87[ASN][1000 genomes]
rs28413125	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28736387	0.87[ASN][1000 genomes]
rs3736488	0.87[ASN][1000 genomes]
rs3765160	0.87[ASN][1000 genomes]
rs3765161	0.87[ASN][1000 genomes]
rs3768659	1.00[ASN][1000 genomes]
rs41263781	1.00[EUR][1000 genomes]
rs41272837	1.00[EUR][1000 genomes]
rs61112771	1.00[EUR][1000 genomes]
rs6711327	1.00[EUR][1000 genomes]
rs6741242	1.00[EUR][1000 genomes]
rs6752549	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73047634	1.00[EUR][1000 genomes]
rs7567045	1.00[EUR][1000 genomes]
rs7576108	0.87[ASN][1000 genomes]
rs7600151	1.00[EUR][1000 genomes]
rs7607614	1.00[EUR][1000 genomes]
rs8224	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv584059	chr2:189841052-189868381	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv875612	chr2:189841052-189878769	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv584060	chr2:189844000-189876138	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv584061	chr2:189844000-189878769	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189841800-189875200	Weak transcription	Colonic Mucosa	Colon
2	chr2:189843600-189874200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:189847600-189879200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:189849400-189877600	Strong transcription	Placenta	Placenta
5	chr2:189849600-189876200	Strong transcription	Stomach Smooth Muscle	stomach
6	chr2:189849800-189871000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:189850400-189877200	Weak transcription	Right Ventricle	heart
8	chr2:189851800-189877200	Strong transcription	Colon Smooth Muscle	Colon
9	chr2:189851800-189878000	Strong transcription	HSMM	muscle
10	chr2:189852000-189877400	Strong transcription	Adipose Nuclei	Adipose
11	chr2:189853200-189874800	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:189853800-189875200	Strong transcription	NHLF	lung
13	chr2:189854000-189878200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:189854200-189876800	Strong transcription	Fetal Lung	lung
15	chr2:189855600-189872800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:189856200-189874200	Strong transcription	Ovary	ovary
17	chr2:189856600-189870600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:189856800-189875400	Weak transcription	Spleen	Spleen
19	chr2:189857200-189875200	Weak transcription	Small Intestine	intestine
20	chr2:189857400-189867800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:189859200-189868800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr2:189859600-189868600	Strong transcription	Fetal Muscle Leg	muscle
23	chr2:189862000-189868200	Weak transcription	Fetal Intestine Small	intestine
24	chr2:189862800-189871200	Weak transcription	Fetal Kidney	kidney
25	chr2:189863400-189867600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:189864200-189871000	Weak transcription	Left Ventricle	heart
27	chr2:189864400-189867600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:189864400-189868600	Weak transcription	Aorta	Aorta
29	chr2:189864400-189877400	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr2:189864600-189867800	Enhancers	Hela-S3	cervix
31	chr2:189864600-189868400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:189865000-189867800	Strong transcription	Fetal Intestine Large	intestine
33	chr2:189865000-189868200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:189865200-189867400	Weak transcription	HSMMtube	muscle
35	chr2:189865200-189874800	Strong transcription	NHDF-Ad	bronchial
36	chr2:189865800-189867400	Genic enhancers	Muscle Satellite Cultured Cells	--
37	chr2:189865800-189873200	Strong transcription	Fetal Stomach	stomach
38	chr2:189866200-189867400	Enhancers	HUVEC	blood vessel
39	chr2:189866200-189867800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:189866400-189867800	Enhancers	NH-A	brain
41	chr2:189866400-189879200	Weak transcription	Gastric	stomach
42	chr2:189866600-189872200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:189866600-189875400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:189866600-189876200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:189866600-189878000	Strong transcription	Osteobl	bone
46	chr2:189866800-189867400	Enhancers	NHEK	skin
47	chr2:189867000-189867400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:189867000-189867400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:189867200-189867400	Enhancers	A549	lung
50	chr2:189867200-189874000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links