Variant report

Variant	rs60502293
Chromosome Location	chr1:171775887-171775888
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	chr1:171755758..171758426-chr1:171775060..171777490,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10798636	0.84[EUR][1000 genomes]
rs10798667	0.92[ASN][1000 genomes]
rs10913644	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11587288	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11590059	0.82[AFR][1000 genomes]
rs12022693	0.82[AFR][1000 genomes]
rs12034454	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12039034	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12566700	0.87[ASN][1000 genomes]
rs16843385	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17597528	0.82[AFR][1000 genomes]
rs2232812	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2232816	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232818	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232826	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294717	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3753538	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56178029	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57476157	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59302445	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60956160	0.84[EUR][1000 genomes]
rs6425423	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425428	0.82[AFR][1000 genomes]
rs6425438	0.92[ASN][1000 genomes]
rs6425439	0.90[ASN][1000 genomes]
rs6684594	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6691222	0.85[ASN][1000 genomes]
rs6695502	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72703115	0.92[ASN][1000 genomes]
rs7541192	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7543608	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7548462	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7860	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs909958	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs941942	0.83[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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60502293	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171766200-171777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:171766400-171777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:171767000-171777200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:171767000-171778600	Weak transcription	NHEK	skin
5	chr1:171767200-171777600	Weak transcription	HMEC	breast
6	chr1:171767400-171777200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:171767800-171778800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:171767800-171781800	Weak transcription	Thymus	Thymus
9	chr1:171768000-171776600	Weak transcription	Esophagus	oesophagus
10	chr1:171768000-171778600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:171768400-171785600	Weak transcription	Gastric	stomach
12	chr1:171770200-171794600	Weak transcription	Primary T cells from cord blood	blood
13	chr1:171770600-171784800	Weak transcription	Primary B cells from cord blood	blood
14	chr1:171771400-171776800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:171771800-171777200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:171773000-171796000	Weak transcription	Pancreas	Pancrea
17	chr1:171774600-171777000	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:171774800-171776600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:171774800-171777600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:171775000-171787000	Weak transcription	Left Ventricle	heart
21	chr1:171775200-171778000	Weak transcription	Aorta	Aorta
22	chr1:171775200-171778200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:171775400-171776000	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:171775400-171777000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:171775400-171777200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:171775400-171779800	Weak transcription	Brain Anterior Caudate	brain
27	chr1:171775400-171783800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:171775600-171776400	Weak transcription	Brain Substantia Nigra	brain
29	chr1:171775600-171776600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:171775600-171777800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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