Variant report

Variant	rs72904915
Chromosome Location	chr2:54227350-54227351
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54214773..54216416-chr2:54226494..54228805,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10188834	0.83[AMR][1000 genomes]
rs10190353	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10199995	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1049894	0.88[AMR][1000 genomes]
rs11125517	0.83[AMR][1000 genomes]
rs11884857	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11886366	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887593	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11889527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890472	0.82[EUR][1000 genomes]
rs11891000	0.82[EUR][1000 genomes]
rs11904365	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395751	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401491	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13401719	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13417051	0.88[AMR][1000 genomes]
rs13432387	0.88[AMR][1000 genomes]
rs2112120	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2161083	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28571698	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28699646	0.88[AMR][1000 genomes]
rs3930909	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs41536750	0.88[AMR][1000 genomes]
rs58920915	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60769690	0.83[AMR][1000 genomes]
rs60776154	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6545382	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6715161	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719990	1.00[AMR][1000 genomes]
rs6723722	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6730494	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745729	0.88[AMR][1000 genomes]
rs6748686	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6751340	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6761648	0.82[EUR][1000 genomes]
rs72906704	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906711	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906714	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7556936	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7559651	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7583508	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7588134	0.87[AMR][1000 genomes]
rs7588319	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7608085	0.88[AMR][1000 genomes]
rs9678301	0.88[AMR][1000 genomes];0.83[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	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54199000-54228800	Weak transcription	Aorta	Aorta
2	chr2:54208400-54248200	Weak transcription	Lung	lung
3	chr2:54211400-54243000	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
5	chr2:54215000-54242800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:54216400-54242000	Weak transcription	Fetal Intestine Small	intestine
7	chr2:54217000-54236600	Weak transcription	Brain Angular Gyrus	brain
8	chr2:54217000-54236800	Weak transcription	Brain Anterior Caudate	brain
9	chr2:54217000-54248200	Weak transcription	Gastric	stomach
10	chr2:54217200-54233800	Weak transcription	HepG2	liver
11	chr2:54217200-54239600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:54222400-54228400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr2:54224400-54239600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:54225200-54228400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:54225600-54228400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:54226000-54231000	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:54226000-54240000	Weak transcription	Primary B cells from cord blood	blood
18	chr2:54226200-54239600	Weak transcription	Adipose Nuclei	Adipose
19	chr2:54226600-54243000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:54226800-54227600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:54226800-54228000	Weak transcription	Right Atrium	heart
22	chr2:54226800-54228200	Weak transcription	Pancreas	Pancrea
23	chr2:54226800-54236800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:54226800-54239000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:54226800-54239200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:54227000-54227400	Weak transcription	Primary T cells from cord blood	blood

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