Variant report

Variant	rs10511625
Chromosome Location	chr9:16693969-16693970
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10511624	0.94[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10733313	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10733314	0.88[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10733315	0.94[CEU][hapmap];0.86[CHB][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10733316	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10738445	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738446	0.89[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10738447	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738448	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10738449	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10756779	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10756781	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10756782	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10756783	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10756784	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10756785	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10756786	0.94[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10756787	0.84[CEU][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10810590	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]
rs10810591	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10810592	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10810593	0.94[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10962542	0.94[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10962546	0.85[CHB][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1337399	0.94[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1888207	0.94[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1888208	0.94[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2026806	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2297174	0.89[CEU][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2297176	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2383002	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2383004	0.94[CEU][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3850444	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3850445	0.94[CEU][hapmap];0.86[CHB][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3861709	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs3904778	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4111334	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4111335	0.94[CEU][hapmap];0.83[CHB][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4360380	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4961732	0.94[CEU][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4961733	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4961734	0.94[CEU][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4961735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4961736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028900	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10511625	PSIP1	cis	cerebellum	SCAN
rs10511625	SH3GL2	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16665000-16704400	Weak transcription	Aorta	Aorta
2	chr9:16679800-16704000	Weak transcription	HSMMtube	muscle
3	chr9:16680000-16704600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:16688200-16700400	Weak transcription	HSMM	muscle
5	chr9:16689800-16699200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:16690000-16701000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr9:16690000-16702400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:16690000-16704200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:16690000-16704800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:16690200-16702000	Weak transcription	NH-A	brain
11	chr9:16690400-16694400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:16690400-16701000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:16690400-16703800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:16690600-16695800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:16690600-16702200	Weak transcription	NHLF	lung
16	chr9:16691000-16694400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:16691000-16694400	Weak transcription	Ovary	ovary
18	chr9:16691000-16701400	Weak transcription	Osteobl	bone
19	chr9:16691000-16704800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:16691000-16708400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:16691200-16694400	Weak transcription	A549	lung
22	chr9:16691200-16695200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:16692400-16695000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:16692400-16695200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr9:16693200-16694200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr9:16693200-16695000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr9:16693200-16695200	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr9:16693400-16694000	Enhancers	Colon Smooth Muscle	Colon
29	chr9:16693400-16694200	Enhancers	HUVEC	blood vessel
30	chr9:16693400-16694600	Enhancers	Fetal Lung	lung
31	chr9:16693400-16694600	Enhancers	Fetal Stomach	stomach
32	chr9:16693400-16694800	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr9:16693600-16695000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr9:16693600-16699000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:16693600-16704600	Weak transcription	Fetal Muscle Leg	muscle

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