Variant report

Variant	rs62280674
Chromosome Location	chr3:101110612-101110613
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	chr3:101105681..101107819-chr3:101109398..101112235,3	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10451923	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511189	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1520654	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16843627	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16843634	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16843699	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16843817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17487	0.82[ASN][1000 genomes]
rs1986294	0.82[ASN][1000 genomes]
rs2271972	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35902489	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3732893	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3773915	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3773917	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3773918	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4260407	0.93[EUR][1000 genomes]
rs4553955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482055	0.80[ASN][1000 genomes]
rs489455	0.82[ASN][1000 genomes]
rs501702	0.82[ASN][1000 genomes]
rs513188	0.82[ASN][1000 genomes]
rs517698	0.82[ASN][1000 genomes]
rs545322	0.82[ASN][1000 genomes]
rs546090	0.82[ASN][1000 genomes]
rs554215	0.82[ASN][1000 genomes]
rs563909	0.82[ASN][1000 genomes]
rs570318	0.82[ASN][1000 genomes]
rs573908	0.82[ASN][1000 genomes]
rs575317	0.82[ASN][1000 genomes]
rs62280636	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62280637	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62280663	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280664	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280665	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62280671	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280720	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280721	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280722	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62280725	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62280726	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280728	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62280731	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62280733	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62280735	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62280737	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62280745	0.94[EUR][1000 genomes]
rs62280747	0.93[EUR][1000 genomes]
rs62282871	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62282873	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62282875	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62282885	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62282886	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62282887	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62282888	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62282889	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62282890	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62282892	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441595	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6796058	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6798685	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72487765	0.81[EUR][1000 genomes]
rs72932462	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7611378	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7621506	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622461	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7632064	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7634592	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9790303	0.94[EUR][1000 genomes];0.82[ASN][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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101045800-101110800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:101085600-101137600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:101096800-101111600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:101099000-101114600	Weak transcription	K562	blood
5	chr3:101106000-101111200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:101106000-101111400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:101106600-101114600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:101106800-101112200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:101106800-101133000	Weak transcription	Left Ventricle	heart
10	chr3:101106800-101133000	Weak transcription	Pancreas	Pancrea
11	chr3:101106800-101133000	Weak transcription	Spleen	Spleen
12	chr3:101107000-101114000	Weak transcription	Fetal Thymus	thymus
13	chr3:101107000-101118600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:101107000-101140800	Weak transcription	Esophagus	oesophagus
15	chr3:101107200-101111600	Weak transcription	Lung	lung
16	chr3:101107200-101133000	Weak transcription	Gastric	stomach
17	chr3:101107200-101133000	Weak transcription	Thymus	Thymus
18	chr3:101107200-101161200	Weak transcription	Aorta	Aorta
19	chr3:101108200-101112600	Weak transcription	Ovary	ovary
20	chr3:101108400-101111400	Weak transcription	Fetal Kidney	kidney
21	chr3:101108600-101111400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:101108600-101111400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:101108600-101112600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:101108600-101113600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:101108600-101114600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:101108600-101114600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:101108600-101116400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:101108600-101119400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:101108600-101138000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:101108800-101111400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:101108800-101113000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:101109400-101133600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:101109600-101111400	Weak transcription	Dnd41	blood
34	chr3:101109800-101127000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:101110200-101114200	ZNF genes & repeats	Primary T cells from cord blood	blood
36	chr3:101110400-101110800	Strong transcription	Primary B cells from cord blood	blood
37	chr3:101110400-101110800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:101110400-101123800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:101110600-101110800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr3:101110600-101111000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:101110600-101111000	ZNF genes & repeats	Fetal Lung	lung
42	chr3:101110600-101113600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:101110600-101124000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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