Variant report

Variant	rs10952289
Chromosome Location	chr7:150524681-150524682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10952288	0.89[JPT][hapmap]
rs13437864	0.89[JPT][hapmap]
rs2110001	0.84[EUR][1000 genomes]
rs4725367	0.89[JPT][hapmap]
rs4725950	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4725951	0.89[JPT][hapmap]
rs6464110	0.83[AFR][1000 genomes]
rs6977081	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs6977416	0.81[EUR][1000 genomes]
rs7787744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7794796	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10952289	XRCC2	cis	cerebellum	SCAN
rs10952289	TMEM176A	cis	parietal	SCAN
rs10952289	ZNF767	cis	cerebellum	SCAN
rs10952289	LHFP	trans	lymphoblastoid	seeQTL
rs10952289	ZNF775	cis	parietal	SCAN
rs10952289	PDIA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150503400-150528000	Weak transcription	Ovary	ovary
2	chr7:150519800-150525200	Enhancers	Fetal Heart	heart
3	chr7:150522400-150542800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:150523400-150528000	Weak transcription	Right Atrium	heart
5	chr7:150523800-150524800	Enhancers	Duodenum Mucosa	Duodenum
6	chr7:150523800-150527600	Weak transcription	Stomach Mucosa	stomach
7	chr7:150523800-150528000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:150524000-150524800	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr7:150524000-150527600	Weak transcription	Fetal Intestine Large	intestine
10	chr7:150524200-150524800	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr7:150524600-150526200	Weak transcription	Liver	Liver
12	chr7:150524600-150526200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:150524600-150527600	Weak transcription	Fetal Intestine Small	intestine

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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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