Variant report

Variant	rs7563574
Chromosome Location	chr2:160968008-160968009
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:160964387..160968256-chr2:161077211..161080822,5	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10171644	0.84[YRI][hapmap]
rs10197183	0.93[YRI][hapmap]
rs10454740	0.84[CEU][hapmap]
rs10497208	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10929970	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11885142	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887337	0.84[CEU][hapmap]
rs11895959	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902965	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13027372	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13403826	0.82[YRI][hapmap]
rs13413256	0.96[YRI][hapmap]
rs13426637	0.93[YRI][hapmap]
rs1457235	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1457236	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs1457237	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1457238	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1457239	0.96[YRI][hapmap]
rs16844824	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1902622	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2061290	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2124971	0.92[YRI][hapmap]
rs2290706	0.92[YRI][hapmap]
rs2357773	0.80[CEU][hapmap]
rs2357861	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2667033	0.81[CEU][hapmap]
rs2715929	0.84[CEU][hapmap]
rs34064895	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34955537	0.82[ASN][1000 genomes]
rs35271738	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35720878	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35859214	0.81[ASN][1000 genomes]
rs3755547	0.93[YRI][hapmap]
rs3796103	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233679	0.85[CEU][hapmap]
rs4265965	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324285	0.85[CEU][hapmap]
rs4426486	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4473342	0.96[YRI][hapmap]
rs4580348	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4664313	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4664314	0.86[ASN][1000 genomes]
rs4664315	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4665160	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6432593	0.84[CEU][hapmap]
rs6432600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6432601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6432602	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6432603	0.80[CEU][hapmap]
rs6729540	0.84[CEU][hapmap]
rs6735425	0.82[AFR][1000 genomes]
rs6747699	0.81[YRI][hapmap]
rs6758074	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs7422400	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs748427	0.84[CEU][hapmap]
rs7558296	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7558852	0.85[CEU][hapmap]
rs7568816	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7569555	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7579481	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7583743	0.80[CEU][hapmap]
rs7584446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7586660	0.96[YRI][hapmap]
rs7596372	0.93[YRI][hapmap]
rs7599127	0.81[AFR][1000 genomes]
rs7608267	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs897832	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs996112	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459929	chr2:160963603-161079435	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv583497	chr2:160963603-161079435	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875346	chr2:160965335-161044155	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1001502	chr2:160967864-161079450	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160953200-160970800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:160954600-160970800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:160954600-160993000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr2:160955800-160968800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:160957000-160970200	Weak transcription	Pancreas	Pancrea
6	chr2:160957400-160981200	Weak transcription	Lung	lung
7	chr2:160959200-161004200	Weak transcription	Gastric	stomach
8	chr2:160959400-160985200	Weak transcription	Esophagus	oesophagus
9	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
10	chr2:160962400-160970800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:160962800-160971000	Strong transcription	Placenta Amnion	Placenta Amnion
12	chr2:160963800-160969200	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:160964200-160993600	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:160964400-160993600	Weak transcription	Fetal Intestine Large	intestine
15	chr2:160964800-160970800	Weak transcription	Stomach Mucosa	stomach
16	chr2:160965000-160968200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:160965600-160969200	Genic enhancers	HMEC	breast
18	chr2:160965800-160969600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:160966200-160969000	Strong transcription	Fetal Intestine Small	intestine
20	chr2:160966400-160968600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:160966400-160970600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:160966400-160980200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:160967000-160968400	Enhancers	GM12878-XiMat	blood
24	chr2:160967000-160969400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:160967200-160970400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:160967200-160979000	Weak transcription	HSMM	muscle
27	chr2:160967400-160968200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr2:160967400-160968800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:160967600-160970400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:160967600-160970800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:160968000-160968600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:160968000-160970200	Weak transcription	NHEK	skin

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