Variant report

Variant	rs1868414
Chromosome Location	chr3:158962641-158962642
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158845961..158848346-chr3:158960432..158962749,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10936173	0.81[CHB][hapmap]
rs10936175	0.81[JPT][hapmap]
rs10936176	0.81[JPT][hapmap]
rs11924990	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs13326945	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs1449017	0.80[CEU][hapmap]
rs1449021	0.82[ASN][1000 genomes]
rs1823311	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2122147	0.98[ASN][1000 genomes]
rs2365490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6441253	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6777541	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap]
rs6781221	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6791853	0.81[JPT][hapmap]
rs720397	1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs7630467	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs7639608	0.80[CEU][hapmap]
rs7639623	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9283610	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9820047	1.00[CHB][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs9821641	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9823142	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9827242	0.97[ASN][1000 genomes]
rs9827400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9829189	0.82[ASN][1000 genomes]
rs9831067	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9834328	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9838646	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap]
rs9839112	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs9852196	0.98[ASN][1000 genomes]
rs9853995	0.80[CEU][hapmap]
rs9856166	0.81[CHB][hapmap]
rs9862769	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs9880642	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3426016	chr3:158676623-158979242	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1868414	ARL14	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158955200-158968800	Weak transcription	NH-A	brain
2	chr3:158955400-158964200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:158957400-158962800	Weak transcription	NHLF	lung
4	chr3:158957400-158969800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:158961800-158963000	Enhancers	Pancreatic Islets	Pancreatic Islet

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