Variant report

Variant	rs2254720
Chromosome Location	chr1:172246865-172246866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172244637..172247504-chr1:172250088..172253023,2	MCF-7	breast:
2	chr1:172235115..172238078-chr1:172246483..172247996,2	MCF-7	breast:
3	chr1:172223524..172225386-chr1:172246377..172249330,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10752923	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12096225	0.91[ASN][1000 genomes]
rs12097276	0.88[ASN][1000 genomes]
rs2251991	1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs2254703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254810	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255076	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2256059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2422076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422077	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2586390	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586395	0.91[ASN][1000 genomes]
rs2586396	0.91[ASN][1000 genomes]
rs2586398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2586399	0.85[ASN][1000 genomes]
rs2586400	0.91[ASN][1000 genomes]
rs2586402	0.91[ASN][1000 genomes]
rs2586405	0.91[ASN][1000 genomes]
rs2586406	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2586409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2586414	0.91[ASN][1000 genomes]
rs2586417	0.91[ASN][1000 genomes]
rs2586418	0.91[ASN][1000 genomes]
rs2586419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2586422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2586423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2586425	0.91[ASN][1000 genomes]
rs2586426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2757486	0.91[ASN][1000 genomes]
rs2757487	0.91[ASN][1000 genomes]
rs2757488	0.91[ASN][1000 genomes]
rs2757489	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2757490	0.88[CHB][hapmap];0.91[ASN][1000 genomes]
rs2757491	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2757492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2757497	0.91[ASN][1000 genomes]
rs2757498	0.91[ASN][1000 genomes]
rs2757499	0.91[ASN][1000 genomes]
rs2757500	1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs2757501	0.88[ASN][1000 genomes]
rs2757502	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2757505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757506	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61807830	0.91[ASN][1000 genomes]
rs61807832	0.91[ASN][1000 genomes]
rs6424867	0.91[ASN][1000 genomes]
rs6677550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702094	0.89[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.83[ASN][1000 genomes]
rs73044902	0.91[ASN][1000 genomes]
rs74124018	0.91[ASN][1000 genomes]
rs9425269	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425271	0.91[ASN][1000 genomes]
rs9425284	0.91[ASN][1000 genomes]
rs9425285	0.91[ASN][1000 genomes]
rs9425544	0.91[ASN][1000 genomes]
rs9633302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv465650	chr1:172175115-172247127	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv548192	chr1:172175115-172247127	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172236200-172247000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:172239000-172262000	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:172240000-172247600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:172240200-172247400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:172243400-172247000	Weak transcription	Fetal Lung	lung
6	chr1:172244200-172247600	Weak transcription	Pancreas	Pancrea
7	chr1:172244400-172247000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:172245600-172247200	Weak transcription	A549	lung
9	chr1:172246000-172249600	Enhancers	NHDF-Ad	bronchial
10	chr1:172246200-172247600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:172246200-172249200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:172246200-172249400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:172246200-172249400	Enhancers	NH-A	brain
14	chr1:172246400-172247200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr1:172246400-172247400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr1:172246400-172247400	Weak transcription	Fetal Intestine Large	intestine
17	chr1:172246400-172247400	Weak transcription	Fetal Intestine Small	intestine
18	chr1:172246400-172247800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:172246400-172248200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:172246400-172249600	Enhancers	Osteobl	bone
21	chr1:172246600-172247400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:172246600-172247600	Weak transcription	HSMM	muscle
23	chr1:172246600-172248000	Enhancers	HSMMtube	muscle
24	chr1:172246600-172248200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:172246600-172249200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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