Variant report

Variant	rs1491981
Chromosome Location	chr3:151040834-151040835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:151037228..151038869-chr3:151040809..151042718,2	MCF-7	breast:
2	chr3:151013951..151016026-chr3:151038369..151040952,2	MCF-7	breast:
3	chr3:151039875..151042217-chr3:151061873..151064664,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10935838	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11922647	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1352887	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1388619	0.88[ASN][1000 genomes]
rs1388622	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1388623	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1388624	0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs1388626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1463727	0.84[CEU][hapmap]
rs1466684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1472121	0.85[CEU][hapmap]
rs1491978	0.93[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs1491979	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1491980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1873619	0.85[CEU][hapmap]
rs1873622	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1907637	0.84[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2046934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2141631	1.00[YRI][hapmap]
rs2172249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2242353	0.85[CEU][hapmap]
rs2870517	0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3732762	0.88[ASN][1000 genomes]
rs3732764	0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3821667	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];0.96[ASN][1000 genomes]
rs3971191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3975401	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3975403	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3975404	0.83[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4146770	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs4603933	0.84[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4679802	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680374	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440731	0.94[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6440732	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440735	0.85[CEU][hapmap]
rs6440739	0.84[CEU][hapmap]
rs6763983	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6767266	0.85[CEU][hapmap]
rs6769397	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6782212	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6790748	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6803224	0.85[CEU][hapmap]
rs6809388	0.92[JPT][hapmap]
rs6809699	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6809705	0.85[JPT][hapmap]
rs7611328	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7615865	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7616382	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs7620353	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7621876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7623356	0.85[CEU][hapmap]
rs7633362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937124	0.83[CEU][hapmap]
rs9820422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9849395	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs9863821	1.00[ASW][hapmap];0.85[CEU][hapmap]
rs9863983	0.85[CEU][hapmap]
rs9864095	0.85[CEU][hapmap]
rs9865758	0.85[CEU][hapmap]
rs9877389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878459	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	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
rs1491981	CLRN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151002600-151044000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:151036000-151044600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:151036200-151043000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:151036600-151045200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:151037200-151044000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr3:151038800-151046400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:151039000-151041800	Weak transcription	HMEC	breast
8	chr3:151039000-151045200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:151039000-151045200	Weak transcription	NHEK	skin
10	chr3:151039000-151045200	Weak transcription	NHLF	lung
11	chr3:151039200-151045200	Weak transcription	Hela-S3	cervix
12	chr3:151039600-151041200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:151039600-151043600	Weak transcription	Adipose Nuclei	Adipose
14	chr3:151039800-151045200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:151040200-151041000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:151040200-151043400	Weak transcription	Primary B cells from cord blood	blood
17	chr3:151040400-151042600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:151040800-151041400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:151040800-151041800	Weak transcription	Monocytes-CD14+_RO01746	blood

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