Variant report

Variant	rs3777880
Chromosome Location	chr6:133823458-133823459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A12-2	chr6:133823390-133823818	ENSG00000227954.1
2	lnc-SLC2A12-2	chr6:133823390-133823818	ENSG00000227954.2
3	lnc-SLC2A12-2	chr6:133823390-133823818	NR_109982

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11962716	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11964752	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11968392	1.00[CEU][hapmap]
rs12660521	1.00[CEU][hapmap]
rs12662135	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12663242	0.96[AMR][1000 genomes]
rs12663243	0.82[AMR][1000 genomes]
rs12664235	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17062582	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs17062630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17062634	0.82[AMR][1000 genomes]
rs1855988	1.00[CEU][hapmap]
rs1883388	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179341	0.82[AMR][1000 genomes]
rs3777808	1.00[CEU][hapmap]
rs3777822	1.00[CEU][hapmap]
rs3777828	1.00[CEU][hapmap]
rs3777856	1.00[CEU][hapmap]
rs3777868	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs3777869	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs3777871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777872	0.82[AMR][1000 genomes]
rs3777873	1.00[CEU][hapmap]
rs3777874	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs3777878	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];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777883	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777884	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777885	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs3822936	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3822937	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs3886686	0.82[AMR][1000 genomes]
rs58073338	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59342392	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60226395	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6899314	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6905892	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs6921578	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73544971	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73544989	0.82[AMR][1000 genomes]
rs73544998	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73544999	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73546803	0.82[AMR][1000 genomes]
rs73546821	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750265	0.91[ASW][hapmap]
rs7773315	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs970984	1.00[CEU][hapmap]
rs970985	1.00[CEU][hapmap]

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133818400-133828400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:133819800-133824000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:133820600-133823600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:133820800-133824200	Enhancers	Fetal Muscle Leg	muscle
5	chr6:133821400-133823800	Weak transcription	Right Atrium	heart
6	chr6:133821400-133824800	Enhancers	Hela-S3	cervix
7	chr6:133821600-133824400	Enhancers	Ovary	ovary
8	chr6:133821600-133824800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr6:133821800-133826600	Enhancers	Adipose Nuclei	Adipose
10	chr6:133821800-133835600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:133822200-133823600	Weak transcription	Left Ventricle	heart
12	chr6:133822200-133826800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:133822600-133824600	Enhancers	HSMM	muscle
14	chr6:133822600-133826800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:133822600-133826800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:133822800-133824600	Enhancers	Fetal Lung	lung
17	chr6:133822800-133826400	Enhancers	Osteobl	bone
18	chr6:133823000-133823600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:133823000-133824400	Enhancers	Fetal Stomach	stomach
20	chr6:133823000-133824600	Enhancers	Fetal Heart	heart
21	chr6:133823000-133824600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr6:133823000-133824600	Enhancers	NHLF	lung
23	chr6:133823000-133824800	Enhancers	NHDF-Ad	bronchial
24	chr6:133823000-133825600	Enhancers	NH-A	brain
25	chr6:133823000-133826400	Enhancers	Fetal Kidney	kidney
26	chr6:133823200-133823600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:133823200-133824400	Enhancers	Colon Smooth Muscle	Colon
28	chr6:133823200-133869600	Weak transcription	Psoas Muscle	Psoas
29	chr6:133823400-133824400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:133823400-133824400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr6:133823400-133824800	Enhancers	HSMMtube	muscle

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