Variant report

Variant	rs17672913
Chromosome Location	chr1:76812062-76812063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11162121	0.87[JPT][hapmap]
rs11162126	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11162133	0.80[CHB][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap]
rs12060625	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12071740	0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs12075208	0.80[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs12076310	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs1325286	0.82[CHB][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.84[TSI][hapmap]
rs17627490	0.93[JPT][hapmap]
rs4949629	0.93[JPT][hapmap]
rs4949706	0.87[JPT][hapmap]

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	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1006776	chr1:76777323-76899975	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1014231	chr1:76781140-76880630	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17672913	ST6GALNAC3	cis	parietal	SCAN
rs17672913	SLC44A5	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76780200-76813800	Weak transcription	Primary B cells from cord blood	blood
2	chr1:76780600-76817200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:76803600-76817400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:76803600-76817400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:76803800-76817600	Weak transcription	Brain Substantia Nigra	brain
6	chr1:76806200-76813800	Weak transcription	Adipose Nuclei	Adipose
7	chr1:76809200-76812200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:76809400-76818800	Weak transcription	Gastric	stomach
9	chr1:76810000-76814000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:76810400-76814400	Weak transcription	Primary T cells from cord blood	blood
11	chr1:76811400-76814200	Weak transcription	Fetal Brain Male	brain
12	chr1:76811400-76822800	Weak transcription	Fetal Stomach	stomach
13	chr1:76812000-76812200	Weak transcription	Stomach Smooth Muscle	stomach

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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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