Variant report

Variant	rs9864095
Chromosome Location	chr3:151007226-151007227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:151005525..151007235-chr3:151013467..151015003,2	MCF-7	breast:
2	chr3:151000556..151002534-chr3:151004666..151007655,2	K562	blood:
3	chr3:151006710..151009411-chr3:151013071..151015478,2	K562	blood:

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];0.90[YRI][hapmap]
rs1463727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1466684	0.85[CEU][hapmap]
rs1472121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1491980	0.85[CEU][hapmap]
rs1491981	0.85[CEU][hapmap]
rs1873619	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]
rs2046934	0.85[CEU][hapmap];0.90[YRI][hapmap]
rs2242353	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821667	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[YRI][hapmap]
rs3971191	0.85[CEU][hapmap]
rs4146770	0.95[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs4679792	0.86[ASN][1000 genomes]
rs4679802	0.85[CEU][hapmap]
rs4680355	0.86[ASN][1000 genomes]
rs4680374	0.85[CEU][hapmap]
rs58792455	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440731	0.80[CEU][hapmap]
rs6440732	0.85[CEU][hapmap]
rs6440735	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6767266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6769397	0.85[CEU][hapmap]
rs6790748	0.85[CEU][hapmap]
rs6803224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6803841	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6809699	0.85[CEU][hapmap]
rs7611328	0.80[CEU][hapmap]
rs7621876	0.85[CEU][hapmap]
rs7622010	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7623356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7633362	0.85[CEU][hapmap]
rs937124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9820422	0.85[CEU][hapmap]
rs9845034	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9863821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9864216	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9877389	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
rs9864095	CLRN1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150983000-151011000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:150984400-151022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:150999400-151011200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:151002000-151010600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:151002000-151012000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:151002200-151009600	Weak transcription	HMEC	breast
7	chr3:151002200-151010800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:151002400-151018000	Weak transcription	NHLF	lung
9	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:151002800-151007800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:151002800-151010800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:151002800-151011200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:151004400-151009600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:151005200-151014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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