Variant report

Variant	rs17346452
Chromosome Location	chr1:172053287-172053288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172053276..172056114-chr1:172063013..172064771,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10489297	1.00[CHB][hapmap]
rs10910941	1.00[CHB][hapmap]
rs10914141	1.00[JPT][hapmap]
rs11584664	0.84[ASN][1000 genomes]
rs11584955	1.00[CHB][hapmap]
rs11589142	1.00[CHB][hapmap]
rs11589349	0.84[ASN][1000 genomes]
rs12123334	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12129264	1.00[CHB][hapmap]
rs12145177	1.00[JPT][hapmap]
rs16843855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16843860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17277008	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17277127	1.00[CHB][hapmap]
rs17346438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17346473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350579	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17361920	1.00[CHB][hapmap]
rs17472925	1.00[JPT][hapmap]
rs2209096	1.00[CHB][hapmap]
rs2421990	1.00[CHB][hapmap]
rs2421991	1.00[CHB][hapmap]
rs4540689	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593688	1.00[CHB][hapmap]
rs61805853	0.92[ASN][1000 genomes]
rs61807762	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807763	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807784	0.84[ASN][1000 genomes]
rs61807786	0.84[ASN][1000 genomes]
rs61807787	0.84[ASN][1000 genomes]
rs628479	1.00[CHB][hapmap]
rs6694089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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

Variant related diseases (count:1)

Disease	PMID	Source
Height	20881960	GWAS catalog

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172038200-172055400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr1:172038200-172058800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:172040600-172076600	Weak transcription	Brain Angular Gyrus	brain
4	chr1:172041000-172054000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:172041200-172060800	Weak transcription	Brain Substantia Nigra	brain
6	chr1:172041400-172061600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:172041600-172061800	Weak transcription	Brain Anterior Caudate	brain
8	chr1:172041800-172061200	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:172046600-172076800	Weak transcription	Fetal Brain Female	brain
10	chr1:172048000-172083800	Weak transcription	Aorta	Aorta
11	chr1:172049400-172110800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:172049600-172059400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:172049800-172058400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:172052400-172057400	Weak transcription	Fetal Lung	lung
15	chr1:172052400-172059000	Weak transcription	NHEK	skin
16	chr1:172052400-172060800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:172052400-172091600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:172052800-172054200	Weak transcription	Fetal Kidney	kidney
19	chr1:172052800-172054200	Weak transcription	Fetal Stomach	stomach

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