Variant report

Variant	rs2162973
Chromosome Location	chr5:80772960-80772961
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	chr5:80757299..80759638-chr5:80770497..80773294,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10035291	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10036712	0.82[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10041030	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10042201	0.82[CHB][hapmap]
rs10042303	0.91[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10043164	0.81[ASN][1000 genomes]
rs10056711	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068144	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10075648	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942266	0.94[ASN][1000 genomes]
rs10942269	0.85[CHD][hapmap]
rs11739075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740689	0.85[CHD][hapmap]
rs11740719	0.92[CHB][hapmap]
rs11742106	0.80[CEU][hapmap]
rs11949697	0.92[CHB][hapmap]
rs12153000	0.93[JPT][hapmap]
rs12697705	0.83[ASW][hapmap];0.86[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13159500	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13171682	0.98[ASN][1000 genomes]
rs1541830	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2396170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34150522	0.81[ASN][1000 genomes]
rs34699788	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35224297	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805726	0.92[CHB][hapmap]
rs4274955	0.85[CHD][hapmap]
rs4392600	0.85[CHD][hapmap]
rs4513668	0.85[CHD][hapmap]
rs4529168	0.81[CHD][hapmap]
rs6452407	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6452410	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452411	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6452412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452414	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6452415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452416	1.00[JPT][hapmap]
rs6865796	0.90[CEU][hapmap]
rs6866156	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866727	0.90[CEU][hapmap]
rs6866741	0.84[ASN][1000 genomes]
rs6868422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6868748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872793	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874029	0.85[CHD][hapmap]
rs6874237	0.86[ASN][1000 genomes]
rs6874274	0.85[CHD][hapmap]
rs6877102	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878037	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6880200	0.84[JPT][hapmap]
rs6883488	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887937	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897189	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7702047	0.85[CHD][hapmap]
rs7702374	0.90[CEU][hapmap]
rs7711020	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719373	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725126	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7733938	0.82[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7737895	0.90[CEU][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs9293275	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9596	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964102	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs9918175	0.90[CEU][hapmap]

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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1028498	chr5:80712364-80860430	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80703200-80779200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:80735400-80778600	Weak transcription	Aorta	Aorta
3	chr5:80739800-80773200	Strong transcription	Fetal Thymus	thymus
4	chr5:80758000-80774000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:80759600-80773200	Strong transcription	Dnd41	blood
6	chr5:80766200-80800000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:80769800-80776400	Weak transcription	Pancreas	Pancrea
8	chr5:80769800-80778600	Weak transcription	K562	blood
9	chr5:80769800-80779600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:80770000-80773000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:80770000-80773400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:80770000-80774400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:80770000-80776200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:80770000-80777600	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:80770000-80778000	Weak transcription	Thymus	Thymus
16	chr5:80770000-80778200	Weak transcription	Primary B cells from cord blood	blood
17	chr5:80770000-80779400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:80770000-80781000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:80770000-80782600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:80770000-80787800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:80770000-80789000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:80770000-80790400	Weak transcription	Right Ventricle	heart
23	chr5:80770000-80797800	Weak transcription	GM12878-XiMat	blood
24	chr5:80770000-80800200	Weak transcription	Brain Anterior Caudate	brain
25	chr5:80770000-80801600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:80770000-80801600	Weak transcription	NHLF	lung
27	chr5:80770000-80803000	Weak transcription	Fetal Kidney	kidney
28	chr5:80770000-80811000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr5:80770000-80812000	Weak transcription	Left Ventricle	heart
30	chr5:80770200-80782600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:80770200-80782600	Weak transcription	Adipose Nuclei	Adipose
32	chr5:80770200-80784200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr5:80770200-80794800	Weak transcription	Fetal Brain Female	brain
34	chr5:80770200-80811000	Weak transcription	Colon Smooth Muscle	Colon
35	chr5:80770400-80774000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr5:80770400-80778000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:80770400-80778000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:80770400-80778400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:80770400-80778600	Weak transcription	Primary T cells from cord blood	blood
40	chr5:80770400-80779400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:80770400-80781400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:80770400-80793600	Weak transcription	Brain Germinal Matrix	brain
43	chr5:80770400-80801600	Weak transcription	Ovary	ovary
44	chr5:80770400-80808200	Weak transcription	Fetal Stomach	stomach
45	chr5:80770600-80778000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr5:80771000-80776400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:80771000-80776600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:80771000-80777800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr5:80771000-80778400	Weak transcription	Fetal Lung	lung
50	chr5:80771000-80780200	Weak transcription	Primary T helper cells fromperipheralblood	blood

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