Variant report

Variant	rs6687139
Chromosome Location	chr1:170173262-170173263
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12118078	1.00[ASN][1000 genomes]
rs12142060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144655	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345893	1.00[ASN][1000 genomes]
rs17345907	1.00[ASN][1000 genomes]
rs17345935	1.00[ASN][1000 genomes]
rs17350032	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17350053	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[ASN][1000 genomes]
rs6662495	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv999310	chr1:170065943-170223350	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	esv3693321	chr1:170167702-170188648	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6687139	C1orf156	cis	lymphoblastoid	seeQTL
rs6687139	SELL	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170170600-170174200	Weak transcription	Osteobl	bone
2	chr1:170170600-170181200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:170172400-170173800	Enhancers	Fetal Heart	heart
4	chr1:170172600-170174600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:170172600-170175400	Enhancers	NHDF-Ad	bronchial
6	chr1:170172800-170173600	Enhancers	Fetal Muscle Leg	muscle
7	chr1:170172800-170174400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:170173000-170173400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:170173000-170174000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:170173000-170174200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:170173000-170174200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:170173000-170174200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:170173200-170173400	Enhancers	Adipose Nuclei	Adipose
14	chr1:170173200-170173600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:170173200-170174000	Enhancers	HUES6 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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