Variant report

Variant	rs1387015
Chromosome Location	chr3:112528969-112528970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11918522	0.90[MEX][hapmap]
rs13064268	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13064475	0.84[ASN][1000 genomes]
rs13064496	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1387021	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1994509	0.81[CHB][hapmap]
rs2399432	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4682434	0.83[ASW][hapmap];0.87[CEU][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes]
rs6773083	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6784658	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7614868	0.98[ASN][1000 genomes]
rs7640561	0.82[CHB][hapmap]
rs9809591	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9835599	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv877343	chr3:112470586-112597706	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1387015	SLC9A10	cis	parietal	SCAN
rs1387015	PHLDB2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112521000-112529800	Weak transcription	A549	lung
2	chr3:112521600-112531600	Weak transcription	Stomach Mucosa	stomach
3	chr3:112526600-112529400	Weak transcription	NHDF-Ad	bronchial
4	chr3:112526600-112530800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:112526800-112529200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:112526800-112529400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:112527000-112531000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:112527000-112531200	Weak transcription	Primary T cells from cord blood	blood
9	chr3:112527400-112530600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:112527400-112532600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:112527600-112530600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:112527600-112531000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:112528200-112529200	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:112528600-112529000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:112528600-112529000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr3:112528800-112530000	Weak transcription	Aorta	Aorta
17	chr3:112528800-112533600	Enhancers	Placenta Amnion	Placenta Amnion

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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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