Variant report

Variant	rs4741560
Chromosome Location	chr9:16043170-16043171
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1014307	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10733306	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10733307	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10738419	0.82[TSI][hapmap]
rs10738420	0.81[CEU][hapmap]
rs10738421	0.82[AMR][1000 genomes]
rs10738423	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10738424	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10738425	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10738426	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10738427	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10738428	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10738430	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10756720	0.85[TSI][hapmap]
rs10756724	0.80[CEU][hapmap]
rs10756726	0.82[CEU][hapmap];0.82[TSI][hapmap]
rs10756728	0.82[TSI][hapmap]
rs10756729	0.84[TSI][hapmap]
rs10756730	0.82[AMR][1000 genomes]
rs10756734	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10756735	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10756736	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10756737	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756738	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10756739	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10756741	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10756742	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10810484	0.85[TSI][hapmap]
rs10810485	0.82[CEU][hapmap]
rs10810488	0.85[TSI][hapmap]
rs10810502	0.82[TSI][hapmap]
rs10810509	0.82[TSI][hapmap]
rs10810517	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10810518	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810519	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10810520	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10810521	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810522	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810523	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810524	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810526	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810527	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810528	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10962260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11788695	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12379466	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1328273	0.83[EUR][1000 genomes]
rs1328274	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1328275	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1328276	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1328277	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1328278	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1328279	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1328280	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1328296	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1328298	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359954	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1359956	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359957	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410444	0.82[CEU][hapmap]
rs1410450	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1410451	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1410452	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1410453	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs1410454	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1410455	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1887666	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1887667	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1887668	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1887669	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1891212	0.87[TSI][hapmap]
rs1984246	0.87[TSI][hapmap]
rs2026661	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2149233	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2382551	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4247294	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4472620	0.81[CEU][hapmap]
rs4740631	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4740632	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4741557	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4741558	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4741559	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4741561	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027202	0.87[TSI][hapmap]
rs7040690	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs752489	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs752490	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs769151	0.82[TSI][hapmap]
rs7873925	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs943787	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs943788	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs943789	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs961117	0.82[CEU][hapmap]
rs9792412	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs997410	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892637	chr9:15926508-16060746	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831521	chr9:15974174-16106565	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1025555	chr9:16022186-16064158	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2761506	chr9:16040491-16093736	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4741560	C9orf93	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16030800-16050000	Weak transcription	Aorta	Aorta
2	chr9:16034000-16043600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:16039800-16043400	Weak transcription	Osteobl	bone
4	chr9:16040000-16043600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:16040400-16043600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:16040600-16057600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:16040800-16043400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:16041200-16044800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:16041200-16049600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:16041400-16043400	Weak transcription	Fetal Kidney	kidney
11	chr9:16041400-16043800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:16041400-16043800	Weak transcription	Fetal Lung	lung
13	chr9:16041400-16044000	Weak transcription	NH-A	brain
14	chr9:16041400-16044600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:16041400-16045400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:16041400-16046200	Weak transcription	Fetal Intestine Large	intestine
17	chr9:16041400-16048000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:16042400-16043600	Weak transcription	Adipose Nuclei	Adipose
19	chr9:16042600-16043600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:16042600-16043800	Weak transcription	Fetal Muscle Leg	muscle
21	chr9:16042600-16044600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:16042800-16043200	Weak transcription	Fetal Stomach	stomach
23	chr9:16042800-16044000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr9:16043000-16043400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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