Variant report

Variant	rs1336492
Chromosome Location	chr9:71376291-71376292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10735625	0.88[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs10869442	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11143607	0.87[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11143636	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12345874	0.89[CEU][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12350270	0.81[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1412986	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1537885	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs17482181	0.81[GIH][hapmap]
rs2027204	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2152647	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4504703	0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs58384767	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7031263	0.88[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs7035163	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7049222	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs7853795	0.95[CEU][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised 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 miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1336492	PIP5K1B	cis	parietal	SCAN
rs1336492	SMC5	cis	cerebellum	SCAN
rs1336492	TJP2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71371200-71384600	Weak transcription	Stomach Mucosa	stomach
2	chr9:71374000-71378000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:71374000-71388800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr9:71374200-71377400	Weak transcription	Primary B cells from cord blood	blood
5	chr9:71375400-71376600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr9:71375800-71376800	Enhancers	K562	blood
7	chr9:71375800-71377400	Weak transcription	Fetal Heart	heart

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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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