Variant report

Variant	rs629109
Chromosome Location	chr6:119446138-119446139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12530153	0.83[CHB][hapmap]
rs1360782	0.83[ASN][1000 genomes]
rs644640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs659466	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6935642	0.93[ASN][1000 genomes]
rs7744514	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9320679	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9481884	0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs629109	NT5DC1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119439200-119448400	Weak transcription	K562	blood
2	chr6:119440600-119448400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:119441400-119449200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:119441400-119450200	Weak transcription	NH-A	brain
5	chr6:119441800-119450400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:119444800-119449600	Weak transcription	Fetal Lung	lung
7	chr6:119445400-119446200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:119445400-119446200	Enhancers	HUVEC	blood vessel
9	chr6:119445400-119446200	Enhancers	NHEK	skin
10	chr6:119445400-119446400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr6:119445600-119446200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr6:119445800-119453400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:119446000-119446200	Enhancers	Stomach Mucosa	stomach
14	chr6:119446000-119450200	Weak transcription	HUES48 Cell Line	embryonic stem cell

Quick Search:

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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