Variant report

Variant	rs3777860
Chromosome Location	chr6:133756500-133756501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A12-4	chr6:133756215-133756708	ENSG00000223542

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11961662	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661876	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12663756	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12664324	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12665147	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12665159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665690	0.87[ASW][hapmap];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];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17062561	1.00[CEU][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2076255	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2076256	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28360637	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3756873	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777853	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3777863	1.00[CEU][hapmap]
rs3798355	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41286198	0.86[EUR][1000 genomes]
rs4895966	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4895967	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55963818	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56088418	0.83[EUR][1000 genomes]
rs56140782	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56182562	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56241016	0.83[EUR][1000 genomes]
rs6922694	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6933900	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73544919	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73544934	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73544945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3777860	STON1	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133732600-133758200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:133749800-133777600	Weak transcription	Hela-S3	cervix
3	chr6:133752400-133763400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:133753800-133757800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:133753800-133757800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:133753800-133758000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr6:133755800-133756800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:133756000-133756800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr6:133756200-133756600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:133756200-133756800	Enhancers	Brain Substantia Nigra	brain
11	chr6:133756400-133756600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr6:133756400-133756600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:133756400-133756600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr6:133756400-133756800	Enhancers	Fetal Muscle Leg	muscle
15	chr6:133756400-133756800	Enhancers	Left Ventricle	heart
16	chr6:133756400-133756800	Enhancers	Right Atrium	heart
17	chr6:133756400-133756800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr6:133756400-133756800	Enhancers	Spleen	Spleen
19	chr6:133756400-133757000	Flanking Active TSS	Liver	Liver
20	chr6:133756400-133757000	Enhancers	HSMMtube	muscle
21	chr6:133756400-133757200	Enhancers	Psoas Muscle	Psoas

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