Variant report

Variant	rs1259061
Chromosome Location	chr6:14999452-14999453
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:13)

rs_ID	r²[population]
rs1259062	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259067	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259068	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259073	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1259074	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1259082	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1268743	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34694507	0.84[EUR][1000 genomes]
rs6459387	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714979	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs724626	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs724627	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv883453	chr6:14926320-15001506	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
rs1259061	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	chr6:14985000-15001600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr6:14985000-15003800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:14985200-15006000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:14985600-15003800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:14986600-15018000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:14993600-15007200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr6:14996000-15001800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:14996200-15003600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:14997400-15001400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:14997400-15002200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:14997600-15001400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:14999000-14999600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:14999200-14999600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:14999200-14999800	Enhancers	NHEK	skin
17	chr6:14999200-15000000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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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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