Variant report

Variant	rs12562173
Chromosome Location	chr1:172059521-172059522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:172059201..172061771-chr1:172370034..172372067,2	MCF-7	breast:
2	chr1:172059250..172060005-chr1:172398255..172399186,4	MCF-7	breast:
3	chr1:172057858..172060800-chr1:172327369..172328971,2	MCF-7	breast:
4	chr1:172058604..172060338-chr1:172368296..172369500,16	MCF-7	breast:
5	chr1:172057836..172060153-chr1:172397391..172399451,2	MCF-7	breast:
6	chr1:172059029..172059772-chr1:172368194..172369295,4	MCF-7	breast:
7	chr1:172057250..172060072-chr1:172060422..172061961,2	K562	blood:
8	chr1:172059494..172060045-chr1:172128380..172129253,2	MCF-7	breast:
9	chr1:172059095..172060013-chr1:172369694..172372109,8	MCF-7	breast:
10	chr1:172047980..172049973-chr1:172059181..172061869,2	K562	blood:
11	chr1:172059051..172060007-chr1:172370843..172371887,3	MCF-7	breast:
12	chr1:171971821..171972449-chr1:172059078..172060039,2	MCF-7	breast:

No data

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10218642	0.94[ASN][1000 genomes]
rs12561987	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12562275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12562403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12564349	1.00[EUR][1000 genomes]
rs12568723	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568908	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12569096	1.00[EUR][1000 genomes]
rs12569236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12569310	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16843769	0.87[JPT][hapmap]
rs16843771	0.88[JPT][hapmap]
rs16843772	0.82[JPT][hapmap]
rs16843775	0.88[JPT][hapmap]
rs16843777	0.88[JPT][hapmap]
rs16843795	0.87[JPT][hapmap]
rs16843801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16843816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16843819	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16843820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16843827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16843831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16843837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16843841	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16843842	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16843915	1.00[EUR][1000 genomes]
rs16843935	1.00[EUR][1000 genomes]
rs34737151	0.91[ASN][1000 genomes]
rs3924561	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4264026	0.91[ASN][1000 genomes]
rs4916417	0.88[JPT][hapmap]
rs4916419	0.88[JPT][hapmap]
rs4916420	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59665490	1.00[EUR][1000 genomes]
rs73039343	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172040600-172076600	Weak transcription	Brain Angular Gyrus	brain
2	chr1:172041200-172060800	Weak transcription	Brain Substantia Nigra	brain
3	chr1:172041400-172061600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:172041600-172061800	Weak transcription	Brain Anterior Caudate	brain
5	chr1:172041800-172061200	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:172046600-172076800	Weak transcription	Fetal Brain Female	brain
7	chr1:172048000-172083800	Weak transcription	Aorta	Aorta
8	chr1:172049400-172110800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:172052400-172060800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:172052400-172091600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:172057800-172060600	Weak transcription	Ovary	ovary
12	chr1:172057800-172074000	Weak transcription	Fetal Lung	lung
13	chr1:172058800-172060000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:172059000-172059600	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:172059200-172059600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr1:172059200-172059600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:172059200-172059600	Active TSS	Duodenum Mucosa	Duodenum
18	chr1:172059200-172059600	Active TSS	Fetal Intestine Large	intestine
19	chr1:172059200-172059600	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr1:172059200-172059600	Enhancers	Rectal Smooth Muscle	rectum
21	chr1:172059200-172059600	Enhancers	A549	lung
22	chr1:172059200-172059600	Flanking Active TSS	NHEK	skin
23	chr1:172059400-172059600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:172059400-172059600	Enhancers	Fetal Stomach	stomach
25	chr1:172059400-172059800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:172059400-172060000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:172059400-172060000	Enhancers	Fetal Intestine Small	intestine

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