Variant report

Variant	rs17292943
Chromosome Location	chr2:189847300-189847301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189840465..189844920-chr2:189846827..189849857,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221502	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12693525	0.88[EUR][1000 genomes]
rs13306261	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13306272	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]
rs16830973	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs17358825	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1800255	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1878201	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1878202	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1914037	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs2203602	0.86[CHB][hapmap]
rs2351420	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736487	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736489	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]
rs3736490	0.95[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41263753	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41265557	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62181727	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6715268	0.93[CHB][hapmap]
rs7596514	0.86[CHB][hapmap];0.81[CHD][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459992	chr2:189796272-189855943	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv584057	chr2:189796272-189855943	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875609	chr2:189796272-189862097	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	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
5	nsv584058	chr2:189799499-189855943	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	esv3418829	chr2:189843907-189847705	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	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
12	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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189838200-189849400	Active TSS	Fetal Muscle Leg	muscle
2	chr2:189839400-189858000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:189841400-189864000	Weak transcription	Left Ventricle	heart
4	chr2:189841800-189875200	Weak transcription	Colonic Mucosa	Colon
5	chr2:189842400-189866600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:189843000-189849400	Weak transcription	Placenta	Placenta
7	chr2:189843400-189861800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:189843600-189874200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:189844400-189849400	Weak transcription	Fetal Intestine Large	intestine
10	chr2:189844400-189866200	Weak transcription	Psoas Muscle	Psoas
11	chr2:189844600-189847400	Weak transcription	Right Atrium	heart
12	chr2:189844600-189849400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:189844600-189859000	Weak transcription	Fetal Intestine Small	intestine
14	chr2:189844800-189847400	Weak transcription	Aorta	Aorta
15	chr2:189844800-189848200	Weak transcription	NH-A	brain
16	chr2:189844800-189849200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:189844800-189849400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:189844800-189849400	Weak transcription	Ovary	ovary
19	chr2:189844800-189849400	Weak transcription	A549	lung
20	chr2:189844800-189850800	Enhancers	Rectal Smooth Muscle	rectum
21	chr2:189844800-189851400	Weak transcription	Fetal Kidney	kidney
22	chr2:189844800-189857200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:189845400-189847800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:189845600-189847800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
25	chr2:189845800-189848400	Enhancers	Fetal Lung	lung
26	chr2:189845800-189848400	Active TSS	Fetal Stomach	stomach
27	chr2:189846000-189847800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:189846400-189848000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
29	chr2:189846600-189847400	Weak transcription	HSMM	muscle
30	chr2:189846800-189847600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:189846800-189848000	Genic enhancers	Osteobl	bone
32	chr2:189847000-189847400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:189847000-189847600	Active TSS	Colon Smooth Muscle	Colon
34	chr2:189847200-189847400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:189847200-189847400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr2:189847200-189847600	Enhancers	Placenta Amnion	Placenta Amnion
37	chr2:189847200-189847600	Enhancers	Stomach Smooth Muscle	stomach
38	chr2:189847200-189847600	Active TSS	HSMMtube	muscle
39	chr2:189847200-189848400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:189847200-189848400	Flanking Active TSS	NHLF	lung

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