Variant report

Variant	rs1328280
Chromosome Location	chr9:16030903-16030904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1014307	0.81[EUR][1000 genomes]
rs10733306	0.85[EUR][1000 genomes]
rs10733307	0.85[EUR][1000 genomes]
rs10738419	0.81[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs10738420	0.81[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10738421	0.87[AMR][1000 genomes]
rs10738422	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10738423	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10738424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10738425	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10738426	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10738427	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10738428	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10738430	0.85[EUR][1000 genomes]
rs10756720	0.89[TSI][hapmap]
rs10756722	0.80[CHB][hapmap]
rs10756726	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs10756728	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10756729	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10756730	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10756731	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10756733	0.94[ASN][1000 genomes]
rs10756734	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756735	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10756736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10756737	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10756738	0.89[EUR][1000 genomes]
rs10756739	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10756741	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10756742	0.85[EUR][1000 genomes]
rs10810479	0.80[CEU][hapmap]
rs10810483	0.80[CHB][hapmap]
rs10810484	0.80[CHB][hapmap];0.89[TSI][hapmap]
rs10810485	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs10810488	0.85[CHD][hapmap];0.89[TSI][hapmap]
rs10810494	0.84[CHD][hapmap];0.82[TSI][hapmap]
rs10810501	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10810502	0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs10810506	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10810509	0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs10810510	0.81[AMR][1000 genomes]
rs10810514	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10810517	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10810518	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10810519	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810520	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10810523	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10810524	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10810526	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10810527	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10810528	0.85[EUR][1000 genomes]
rs10962225	0.80[CHB][hapmap]
rs10962244	0.84[ASN][1000 genomes]
rs10962256	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10962260	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11788695	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379466	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1328273	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1328274	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1328275	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1328276	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1328277	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1328278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1328279	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1328283	0.80[CHB][hapmap]
rs1328296	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1328298	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1359951	0.90[ASN][1000 genomes]
rs1359954	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1359956	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1359957	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1410444	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs1410450	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1410451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1410452	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1410453	1.00[CEU][hapmap]
rs1410454	1.00[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1410455	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1887664	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1887666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887667	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1887668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1887669	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1891212	0.82[TSI][hapmap]
rs1927698	0.80[CHB][hapmap]
rs1984246	0.82[TSI][hapmap]
rs2026661	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2149233	0.83[EUR][1000 genomes]
rs2225182	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2382551	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2891003	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2987099	0.84[ASN][1000 genomes]
rs3008707	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3008710	0.84[ASN][1000 genomes]
rs3008715	0.84[ASN][1000 genomes]
rs3008717	0.84[ASN][1000 genomes]
rs3824502	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4247294	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472620	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs4582646	0.80[CHB][hapmap]
rs4740629	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4740631	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4740632	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4741548	0.81[CHB][hapmap]
rs4741552	0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap]
rs4741553	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4741557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4741558	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4741559	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4741560	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4741561	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7027202	0.82[TSI][hapmap]
rs7040690	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs752489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs752490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769151	0.84[CHD][hapmap];0.86[TSI][hapmap]
rs7873925	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs943787	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961117	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs9792412	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs997410	0.89[AMR][1000 genomes];0.97[EUR][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	esv3350040	chr9:16030822-16031153	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1328280	C9orf93	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16022600-16031800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:16023600-16040600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:16026000-16033400	Enhancers	Osteobl	bone
4	chr9:16026200-16039200	Weak transcription	Adipose Nuclei	Adipose
5	chr9:16026400-16033000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:16026400-16039200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:16027000-16031000	Enhancers	NH-A	brain
8	chr9:16027800-16031200	Enhancers	NHDF-Ad	bronchial
9	chr9:16028200-16032000	Enhancers	NHLF	lung
10	chr9:16028200-16033000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:16028600-16032800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:16028600-16033000	Enhancers	HMEC	breast
13	chr9:16028800-16032200	Enhancers	Dnd41	blood
14	chr9:16029000-16031600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:16029000-16031600	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:16029200-16033400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr9:16029400-16031600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:16029400-16032000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr9:16029600-16031600	Enhancers	Hela-S3	cervix
20	chr9:16029600-16033000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:16030000-16031200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:16030200-16031000	Enhancers	Primary hematopoietic stem cells	blood
23	chr9:16030200-16032600	Enhancers	HSMMtube	muscle
24	chr9:16030400-16031000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:16030400-16032400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr9:16030400-16034400	Enhancers	NHEK	skin
27	chr9:16030600-16031000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:16030600-16031000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr9:16030600-16031000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:16030600-16031200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:16030600-16031200	Enhancers	HUVEC	blood vessel
32	chr9:16030600-16032000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr9:16030600-16033400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:16030800-16031200	Flanking Active TSS	HSMM	muscle
35	chr9:16030800-16031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:16030800-16050000	Weak transcription	Aorta	Aorta

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