Variant report

Variant	rs6459387
Chromosome Location	chr6:15002358-15002359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1259061	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259062	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259063	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259068	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259073	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259074	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1259082	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1268743	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34694507	0.89[EUR][1000 genomes]
rs4715957	0.84[EUR][1000 genomes]
rs714979	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs724626	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs724627	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031668	chr6:14774036-15044308	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538138	chr6:14774036-15044308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv970723	chr6:14997807-15023765	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6459387	TBC1D7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:14976000-15006400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:14984600-15006600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:14985000-15003800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:14985200-15006000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:14985600-15003800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:14986600-15018000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:14993600-15007200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:14996200-15003600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:15001200-15003200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:15001400-15002400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:15001600-15002400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:15001600-15002400	Enhancers	Fetal Muscle Leg	muscle
13	chr6:15001800-15002800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:15001800-15009200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:15002000-15002400	Enhancers	Fetal Lung	lung
16	chr6:15002000-15003000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:15002200-15004200	Strong transcription	H9 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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