Variant report

Variant	rs10510830
Chromosome Location	chr3:60131360-60131361
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11130756	0.97[ASN][1000 genomes]
rs11709255	0.83[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs12632865	0.94[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12638226	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17062350	0.94[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap]
rs17062353	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61158509	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62240251	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62240252	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62240253	0.94[ASN][1000 genomes]
rs62240254	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62240255	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7630823	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7642242	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2752010	chr3:60067396-60288428	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1009063	chr3:60067866-60277128	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1013919	chr3:60067866-60284882	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv519855	chr3:60068730-60276722	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv460566	chr3:60068730-60276722	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv460567	chr3:60068730-60276722	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv590390	chr3:60068730-60276722	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv590391	chr3:60068730-60277709	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1008586	chr3:60070974-60258108	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv536576	chr3:60070974-60258108	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1009971	chr3:60070974-60397331	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1008267	chr3:60071947-60264461	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1007798	chr3:60071947-60277128	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv2763751	chr3:60071959-60292312	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv2752011	chr3:60073153-60288428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv432421	chr3:60073153-60288428	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv876840	chr3:60083293-60194570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv915646	chr3:60088475-60240653	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv1003632	chr3:60095363-60258108	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv536577	chr3:60095363-60258108	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv1010969	chr3:60124962-60425297	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10510830	PTPRG	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60123400-60141200	Weak transcription	Pancreas	Pancrea
2	chr3:60124800-60145400	Weak transcription	Thymus	Thymus
3	chr3:60127800-60131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:60128000-60131600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:60128000-60132000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:60128000-60132000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:60128200-60132200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:60128400-60132400	Weak transcription	Psoas Muscle	Psoas
9	chr3:60130600-60131400	Enhancers	Brain Substantia Nigra	brain
10	chr3:60131000-60131600	Enhancers	Brain Angular Gyrus	brain
11	chr3:60131000-60132400	Enhancers	Brain Anterior Caudate	brain
12	chr3:60131000-60133600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:60131000-60133600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr3:60131200-60132000	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:60131200-60133600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:60131200-60133800	Enhancers	Brain Hippocampus Middle	brain

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