Variant report

Variant	rs3736489
Chromosome Location	chr2:189867844-189867845
allele	A/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	chr2:189866735-189869543	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: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12693525	0.81[EUR][1000 genomes]
rs13306261	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13306270	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13306272	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]
rs16830973	0.81[EUR][1000 genomes]
rs17292943	0.95[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17358825	0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800255	0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1878201	0.87[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs1878202	0.85[ASN][1000 genomes]
rs1914037	0.80[EUR][1000 genomes]
rs2203602	0.86[CHB][hapmap]
rs2351420	0.89[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3736487	0.95[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3736490	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41263753	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41265557	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62181727	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7596514	0.89[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[LWK][hapmap]

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:45 , 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	chr2:189859200-189868800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:189859600-189868600	Strong transcription	Fetal Muscle Leg	muscle
22	chr2:189862000-189868200	Weak transcription	Fetal Intestine Small	intestine
23	chr2:189862800-189871200	Weak transcription	Fetal Kidney	kidney
24	chr2:189864200-189871000	Weak transcription	Left Ventricle	heart
25	chr2:189864400-189868600	Weak transcription	Aorta	Aorta
26	chr2:189864400-189877400	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr2:189864600-189868400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:189865000-189868200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:189865200-189874800	Strong transcription	NHDF-Ad	bronchial
30	chr2:189865800-189873200	Strong transcription	Fetal Stomach	stomach
31	chr2:189866400-189879200	Weak transcription	Gastric	stomach
32	chr2:189866600-189872200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:189866600-189875400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:189866600-189876200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:189866600-189878000	Strong transcription	Osteobl	bone
36	chr2:189867200-189874000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:189867400-189869200	Strong transcription	Rectal Smooth Muscle	rectum
38	chr2:189867400-189876000	Strong transcription	HSMMtube	muscle
39	chr2:189867400-189878000	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr2:189867600-189874000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:189867600-189878400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:189867800-189868800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:189867800-189868800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:189867800-189870800	Weak transcription	Fetal Intestine Large	intestine
45	chr2:189867800-189871000	Weak transcription	NH-A	brain

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