Variant report

Variant	rs12039815
Chromosome Location	chr1:212355971-212355972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10779574	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863952	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119875	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358452	0.87[AFR][1000 genomes]
rs351385	0.83[JPT][hapmap]
rs6540731	0.85[GIH][hapmap]
rs6540732	0.85[GIH][hapmap]
rs6679064	0.87[AFR][1000 genomes]
rs7519168	0.85[GIH][hapmap]

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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12039815	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs12039815	SYT14	cis	cerebellum	SCAN
rs12039815	NUAK2	trans	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212336800-212359600	Weak transcription	Dnd41	blood
2	chr1:212350600-212359600	Weak transcription	K562	blood
3	chr1:212352600-212357200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr1:212352600-212357200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:212352800-212356000	Weak transcription	Adipose Nuclei	Adipose
6	chr1:212353000-212357400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:212353000-212357400	Weak transcription	Spleen	Spleen
8	chr1:212353000-212361200	Weak transcription	Right Atrium	heart
9	chr1:212353200-212357400	Weak transcription	Placenta	Placenta
10	chr1:212353200-212361200	Weak transcription	Lung	lung
11	chr1:212354000-212360400	Weak transcription	Esophagus	oesophagus
12	chr1:212354200-212359800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:212354200-212360000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:212354200-212361200	Weak transcription	HMEC	breast
15	chr1:212355200-212361200	Weak transcription	Left Ventricle	heart
16	chr1:212355600-212356000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr1:212355600-212357800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:212355800-212356200	Enhancers	Skeletal Muscle Male	skeletal muscle

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Input of quick search could be:

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

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