Variant report

Variant	rs1523517
Chromosome Location	chr3:121726991-121726992
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121725712..121729014-chr3:121739125..121742417,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145103	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10934569	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10934570	0.86[CHB][hapmap]
rs1143670	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs1143671	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs1143672	1.00[CHB][hapmap]
rs11718322	0.87[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs11914993	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs11920521	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs11924058	0.87[EUR][1000 genomes]
rs11929195	0.81[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs11929235	0.81[CHB][hapmap]
rs1316397	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs1357531	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs1920319	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs2001212	0.87[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2049330	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs2049331	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs2141615	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs2257115	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs2257119	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs2257132	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs2257212	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs2257214	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs2293614	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs2293616	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs2332032	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2332036	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2332046	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs2689283	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs2700420	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs2700421	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs2877566	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs2877568	0.94[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap]
rs3762819	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs3762821	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs3805134	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs3805138	1.00[CHB][hapmap]
rs3915061	0.87[CHB][hapmap]
rs4974395	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974396	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4974397	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6438687	0.94[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap]
rs6803757	0.94[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap]
rs7637569	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs866926	0.94[CHB][hapmap]
rs866927	0.94[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap]
rs874741	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs874742	1.00[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs9289182	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs9289183	0.94[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap]
rs9812515	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs9816720	0.94[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs9830721	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs9862977	1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs9868257	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.96[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	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1523517	GOLGB1	cis	multi-tissue	Pritchard
rs1523517	SLC15A2	cis	cerebellum	SCAN
rs1523517	EAF2	cis	cerebellum	SCAN
rs1523517	IQCB1	cis	parietal	SCAN
rs1523517	SLC15A2	cis	parietal	SCAN
rs1523517	IQCB1	cis	cerebellum	SCAN
rs1523517	SLC15A2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121705200-121729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:121713000-121732200	Weak transcription	Esophagus	oesophagus
3	chr3:121720800-121732200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:121720800-121732200	Weak transcription	Pancreas	Pancrea
5	chr3:121722000-121732400	Weak transcription	Colonic Mucosa	Colon
6	chr3:121722200-121732200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:121723200-121731800	Weak transcription	NHEK	skin
8	chr3:121723800-121728000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:121724000-121728600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:121724000-121731800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:121724200-121740600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:121724400-121728400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:121724400-121732600	Weak transcription	Fetal Intestine Large	intestine
14	chr3:121724600-121733400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:121725400-121728400	Weak transcription	GM12878-XiMat	blood
16	chr3:121726200-121730000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:121726200-121732200	Weak transcription	Fetal Intestine Small	intestine
18	chr3:121726200-121735000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:121726400-121727000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:121726600-121727200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:121726600-121728000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:121726600-121728400	Weak transcription	Rectal Mucosa Donor 29	rectum

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