Variant report

Variant	rs10810590
Chromosome Location	chr9:16689291-16689292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10511624	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs10511625	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10733313	0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10733314	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs10733315	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs10733316	0.83[ASN][1000 genomes]
rs10738445	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[ASN][1000 genomes]
rs10738446	0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs10738447	0.82[ASN][1000 genomes]
rs10738448	0.82[ASN][1000 genomes]
rs10738449	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs10756779	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10756781	0.83[ASN][1000 genomes]
rs10756782	0.83[ASN][1000 genomes]
rs10756783	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs10756786	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs10810591	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10810592	0.82[ASN][1000 genomes]
rs10810593	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs10962542	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs10962546	0.85[CHB][hapmap]
rs1888207	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs1888208	0.83[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2026806	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2297176	0.86[CHB][hapmap]
rs2383002	0.86[ASN][1000 genomes]
rs3850444	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3850445	0.86[CHB][hapmap]
rs3904778	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4111335	0.83[CHB][hapmap]
rs4360380	0.82[ASN][1000 genomes]
rs4961732	0.84[ASN][1000 genomes]
rs4961733	0.84[ASN][1000 genomes]
rs4961734	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4961735	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4961736	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7028900	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv892649	chr9:16677221-16761597	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1030598	chr9:16680138-16696510	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10810590	PSIP1	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16665000-16704400	Weak transcription	Aorta	Aorta
2	chr9:16679600-16693600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:16679800-16689400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr9:16679800-16704000	Weak transcription	HSMMtube	muscle
5	chr9:16680000-16704600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:16681800-16689400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr9:16682200-16689400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:16683400-16689800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:16683800-16689400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:16684600-16690200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:16686800-16691200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:16687200-16689600	Enhancers	NHDF-Ad	bronchial
13	chr9:16687200-16690600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:16687400-16689800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:16687400-16690400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:16687600-16690400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:16687800-16689400	Enhancers	HUVEC	blood vessel
18	chr9:16687800-16689800	Enhancers	Fetal Lung	lung
19	chr9:16688000-16689600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:16688000-16690000	Enhancers	Osteobl	bone
21	chr9:16688200-16689400	Weak transcription	Ovary	ovary
22	chr9:16688200-16691000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr9:16688200-16700400	Weak transcription	HSMM	muscle
24	chr9:16688600-16690200	Enhancers	Colon Smooth Muscle	Colon
25	chr9:16688600-16691000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:16688600-16691200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr9:16688600-16691200	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr9:16688800-16689400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:16688800-16689600	Enhancers	Fetal Intestine Large	intestine
30	chr9:16688800-16689800	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr9:16688800-16689800	Enhancers	Rectal Smooth Muscle	rectum
32	chr9:16688800-16690000	Enhancers	H9 Cell Line	embryonic stem cell
33	chr9:16688800-16690000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr9:16688800-16690000	Enhancers	Adipose Nuclei	Adipose
35	chr9:16688800-16690200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr9:16688800-16690200	Enhancers	Fetal Muscle Leg	muscle
37	chr9:16688800-16690200	Enhancers	NH-A	brain
38	chr9:16688800-16690400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr9:16688800-16690600	Enhancers	NHLF	lung
40	chr9:16689000-16689400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:16689000-16690200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr9:16689000-16690400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:16689200-16689400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:16689200-16689600	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr9:16689200-16689600	Enhancers	Fetal Intestine Small	intestine
46	chr9:16689200-16689800	Flanking Active TSS	A549	lung
47	chr9:16689200-16690400	Enhancers	Fetal Stomach	stomach

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