Variant report

Variant	rs6440735
Chromosome Location	chr3:151044732-151044733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:151029737..151031573-chr3:151044175..151046393,2	MCF-7	breast:
2	chr3:151021234..151025100-chr3:151041293..151045950,7	MCF-7	breast:
3	chr3:151042759..151045096-chr3:151054558..151057198,3	K562	blood:
4	chr3:151032337..151036170-chr3:151042057..151045470,4	MCF-7	breast:
5	chr3:151033641..151035853-chr3:151044142..151046293,2	MCF-7	breast:
6	chr3:151021027..151023183-chr3:151044316..151046639,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144893	Chromatin interaction
ENSG00000138271	Chromatin interaction

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

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151036600-151045200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:151038800-151046400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:151039000-151045200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:151039000-151045200	Weak transcription	NHEK	skin
5	chr3:151039000-151045200	Weak transcription	NHLF	lung
6	chr3:151039200-151045200	Weak transcription	Hela-S3	cervix
7	chr3:151039800-151045200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:151041800-151045000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:151042400-151045000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:151042400-151045200	Weak transcription	HMEC	breast
11	chr3:151042600-151046200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:151044000-151045200	Active TSS	Primary hematopoietic stem cells	blood
13	chr3:151044200-151045400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
14	chr3:151044400-151045000	Enhancers	Adipose Nuclei	Adipose
15	chr3:151044400-151045200	Active TSS	Liver	Liver
16	chr3:151044400-151045600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:151044400-151047000	Active TSS	Brain Hippocampus Middle	brain
18	chr3:151044600-151044800	Active TSS	Primary B cells from cord blood	blood
19	chr3:151044600-151045000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr3:151044600-151045200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:151044600-151046200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood

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