Variant report

Variant	rs13306272
Chromosome Location	chr2:189863389-189863390
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	POLR2A	chr2:189863218-189863639	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
COL3A1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12693525	0.84[EUR][1000 genomes]
rs13306261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13306270	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs16830973	0.85[EUR][1000 genomes]
rs17292943	0.95[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17358825	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1800255	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878201	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1878202	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1914037	0.84[EUR][1000 genomes]
rs2203602	0.92[CHB][hapmap]
rs2351420	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3736487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736489	0.88[ASW][hapmap];0.91[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3736490	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41263753	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41265557	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62181727	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715268	0.85[CHB][hapmap]
rs7596514	0.92[CHB][hapmap];0.90[CHD][hapmap];0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv1791841	chr2:189811074-189864582	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription 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
3	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
4	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
5	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
6	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
7	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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189841400-189864000	Weak transcription	Left Ventricle	heart
2	chr2:189841800-189875200	Weak transcription	Colonic Mucosa	Colon
3	chr2:189842400-189866600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:189843600-189874200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:189844400-189866200	Weak transcription	Psoas Muscle	Psoas
6	chr2:189847600-189879200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:189849400-189877600	Strong transcription	Placenta	Placenta
8	chr2:189849600-189876200	Strong transcription	Stomach Smooth Muscle	stomach
9	chr2:189849800-189871000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:189850000-189865000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:189850400-189877200	Weak transcription	Right Ventricle	heart
12	chr2:189851800-189863400	Strong transcription	NHDF-Ad	bronchial
13	chr2:189851800-189863800	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr2:189851800-189877200	Strong transcription	Colon Smooth Muscle	Colon
15	chr2:189851800-189878000	Strong transcription	HSMM	muscle
16	chr2:189852000-189877400	Strong transcription	Adipose Nuclei	Adipose
17	chr2:189852200-189865800	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr2:189853200-189874800	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:189853800-189875200	Strong transcription	NHLF	lung
20	chr2:189854000-189878200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:189854200-189876800	Strong transcription	Fetal Lung	lung
22	chr2:189854600-189865200	Strong transcription	HSMMtube	muscle
23	chr2:189855600-189872800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:189856000-189865000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:189856200-189865000	Strong transcription	Fetal Stomach	stomach
26	chr2:189856200-189874200	Strong transcription	Ovary	ovary
27	chr2:189856600-189870600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:189856800-189875400	Weak transcription	Spleen	Spleen
29	chr2:189857200-189875200	Weak transcription	Small Intestine	intestine
30	chr2:189857400-189867800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:189859200-189868800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:189859600-189868600	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:189860600-189866800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:189861400-189866200	Weak transcription	NH-A	brain
35	chr2:189861400-189866600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:189861600-189864000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:189862000-189864000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:189862000-189868200	Weak transcription	Fetal Intestine Small	intestine
39	chr2:189862200-189864400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:189862200-189866600	Genic enhancers	Osteobl	bone
41	chr2:189862400-189863400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:189862400-189865000	Weak transcription	Fetal Intestine Large	intestine
43	chr2:189862400-189866200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:189862600-189866200	Weak transcription	A549	lung
45	chr2:189862800-189871200	Weak transcription	Fetal Kidney	kidney
46	chr2:189863200-189864000	Weak transcription	Aorta	Aorta
47	chr2:189863200-189865600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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