Variant report

Variant	rs1873619
Chromosome Location	chr3:151018513-151018514
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	chr3:151017110..151019943-chr3:151020802..151024030,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1352887	0.85[CEU][hapmap]
rs1388626	0.85[CEU][hapmap]
rs1463727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1466684	0.85[CEU][hapmap]
rs1472121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1491980	0.85[CEU][hapmap]
rs1491981	0.85[CEU][hapmap]
rs2046934	0.85[CEU][hapmap]
rs2242353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821667	0.85[CEU][hapmap]
rs3971191	0.85[CEU][hapmap]
rs4146770	0.95[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4679792	0.93[ASN][1000 genomes]
rs4679802	0.85[CEU][hapmap]
rs4680355	0.93[ASN][1000 genomes]
rs4680374	0.85[CEU][hapmap]
rs58792455	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440731	0.80[CEU][hapmap]
rs6440732	0.85[CEU][hapmap]
rs6440735	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6767266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769397	0.85[CEU][hapmap]
rs6790748	0.85[CEU][hapmap]
rs6803224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6803841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809699	0.85[CEU][hapmap]
rs7611328	0.80[CEU][hapmap]
rs7621876	0.85[CEU][hapmap]
rs7622010	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7623356	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633362	0.85[CEU][hapmap]
rs937124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9820422	0.85[CEU][hapmap]
rs9845034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9863983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9864095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9864216	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9865758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877389	1.00[ASW][hapmap];0.85[CEU][hapmap]

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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1873619	CLRN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150984400-151022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:151010200-151022200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:151010400-151019000	Strong transcription	NHEK	skin
5	chr3:151010600-151018800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:151011200-151018800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:151011400-151021800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:151011800-151021600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:151012400-151021600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:151012800-151021600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:151014400-151021800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:151014400-151022400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:151014400-151022600	Weak transcription	Esophagus	oesophagus
14	chr3:151015200-151021800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:151017000-151021600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:151017000-151022600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:151017400-151019400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:151018000-151020000	Enhancers	NHLF	lung
19	chr3:151018200-151021600	Genic enhancers	HMEC	breast
20	chr3:151018200-151022000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:151018400-151018600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:151018400-151018800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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