Variant report

Variant	rs12616127
Chromosome Location	chr2:100232743-100232744
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100231861..100234542-chr2:100254198..100256045,2	MCF-7	breast:
2	chr2:100231974..100233617-chr2:100236243..100238101,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EIF5B-4	chr2:100231958-100234378	NONHSAT072763

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11123789	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895560	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11900988	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11901863	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12474603	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12612124	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712052	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1916959	0.83[AMR][1000 genomes]
rs2309728	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34112064	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792128	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4568000	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4850908	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55989048	0.89[ASN][1000 genomes]
rs6716694	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6722898	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558495	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7561197	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7561948	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7567996	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9973326	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9973472	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12616127	LYG1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100211000-100234200	Weak transcription	Thymus	Thymus
2	chr2:100211000-100249600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:100217000-100258400	Weak transcription	Primary T cells from cord blood	blood
4	chr2:100218200-100241400	Weak transcription	Spleen	Spleen
5	chr2:100224800-100237800	Weak transcription	Fetal Lung	lung
6	chr2:100224800-100239800	Weak transcription	Right Ventricle	heart
7	chr2:100226800-100236000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:100230800-100232800	Enhancers	Fetal Muscle Leg	muscle
9	chr2:100230800-100234200	Weak transcription	K562	blood
10	chr2:100231000-100237000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:100231000-100240400	Weak transcription	Fetal Kidney	kidney
12	chr2:100231200-100238600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:100231400-100243400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr2:100231800-100233800	Strong transcription	Primary B cells from cord blood	blood
15	chr2:100232400-100238600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:100232400-100242800	Weak transcription	Lung	lung
17	chr2:100232600-100234400	Weak transcription	Fetal Brain Male	brain

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