Variant report

Variant	rs28555343
Chromosome Location	chr5:98373119-98373120
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	chr5:98372764..98374577-chr5:98390711..98393548,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10039507	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10040675	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10041263	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10041335	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10054523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055595	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10056842	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10056918	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10061406	0.93[EUR][1000 genomes]
rs10062455	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10064594	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10065808	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10067635	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10067866	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10068003	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10068917	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10077697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10085106	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10085145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10479350	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10479351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10479352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10479353	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10479354	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12332280	0.96[EUR][1000 genomes]
rs12332340	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12332364	0.93[EUR][1000 genomes]
rs12332383	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs161742	0.93[EUR][1000 genomes]
rs17166414	0.85[EUR][1000 genomes]
rs17166423	0.85[EUR][1000 genomes]
rs17166439	0.85[EUR][1000 genomes]
rs17166455	0.87[EUR][1000 genomes]
rs17166484	0.91[EUR][1000 genomes]
rs17166575	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17166578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2164986	0.85[EUR][1000 genomes]
rs28656032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2963709	0.91[EUR][1000 genomes]
rs327810	0.81[EUR][1000 genomes]
rs36011435	0.85[EUR][1000 genomes]
rs44070	0.93[EUR][1000 genomes]
rs55780476	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55821667	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55854720	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56046686	0.87[AFR][1000 genomes]
rs56086412	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56096102	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56115002	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56153113	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56159022	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56160758	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56246849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56311403	0.89[AFR][1000 genomes]
rs56331326	0.80[EUR][1000 genomes]
rs56331947	0.91[EUR][1000 genomes]
rs56400831	0.85[EUR][1000 genomes]
rs58479016	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58771325	0.89[EUR][1000 genomes]
rs6596659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6867271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6883467	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6885458	0.82[AFR][1000 genomes]
rs6890358	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6895358	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7708436	0.91[EUR][1000 genomes]
rs7719375	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7737402	0.93[EUR][1000 genomes]
rs9327950	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9327954	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9327955	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024391	chr5:98355665-98653657	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv599118	chr5:98358191-99029453	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv599119	chr5:98358191-99315677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98368800-98373200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:98369200-98373200	Weak transcription	Colonic Mucosa	Colon
3	chr5:98369600-98373200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:98369600-98373200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:98369600-98373400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:98370200-98373400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:98370400-98373200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:98370400-98373200	Weak transcription	Stomach Mucosa	stomach
9	chr5:98370400-98373400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr5:98370400-98373400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr5:98370400-98373600	Weak transcription	Primary B cells from cord blood	blood
12	chr5:98371400-98373800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:98371600-98373200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr5:98371600-98373200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr5:98371600-98373200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr5:98371800-98373200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr5:98372400-98373200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr5:98372800-98373200	Enhancers	Primary T cells from cord blood	blood
19	chr5:98372800-98373200	Enhancers	Dnd41	blood
20	chr5:98372800-98374000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:98372800-98374400	Enhancers	Primary T cells fromperipheralblood	blood
22	chr5:98372800-98374800	Enhancers	Primary B cells from peripheral blood	blood
23	chr5:98373000-98373400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:98373000-98373400	Enhancers	Gastric	stomach
25	chr5:98373000-98373400	Enhancers	K562	blood
26	chr5:98373000-98373600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr5:98373000-98373600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:98373000-98373600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:98373000-98373600	Enhancers	Esophagus	oesophagus
30	chr5:98373000-98373600	Enhancers	Small Intestine	intestine
31	chr5:98373000-98373600	Flanking Active TSS	HepG2	liver
32	chr5:98373000-98373800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:98373000-98373800	Enhancers	Thymus	Thymus
34	chr5:98373000-98374000	Enhancers	Lung	lung
35	chr5:98373000-98374000	Enhancers	GM12878-XiMat	blood
36	chr5:98373000-98374200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr5:98373000-98374200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr5:98373000-98374200	Enhancers	Fetal Thymus	thymus
39	chr5:98373000-98374400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:98373000-98374400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr5:98373000-98375000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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