Variant report

Variant	rs1339221
Chromosome Location	chr1:217172606-217172607
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	chr1:217167662..217170376-chr1:217171384..217173746,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10779288	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs10863285	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs11117745	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs1832523	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1890551	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1890552	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2576196	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2576201	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2576208	0.90[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs2789557	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs2789558	0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs2789560	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2789572	0.94[ASN][1000 genomes]
rs2818768	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2818769	0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2818772	0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2818773	0.94[ASN][1000 genomes]
rs2818798	0.84[ASN][1000 genomes]
rs2818801	0.81[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3000609	0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468149	chr1:217134966-217203091	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv549204	chr1:217134966-217203091	Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1008670	chr1:217155114-217206765	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1012243	chr1:217157000-217206765	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1006155	chr1:217157000-217215465	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1004880	chr1:217157748-217206765	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1011212	chr1:217162443-217206765	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1339221	LQK1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217157400-217194400	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:217170800-217173600	Weak transcription	Left Ventricle	heart

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