Variant report

Variant	rs6478196
Chromosome Location	chr9:118377417-118377418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1006008	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10116519	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10123924	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10124673	0.86[EUR][1000 genomes]
rs10817790	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10817791	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10817792	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10817802	0.92[EUR][1000 genomes]
rs10982789	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10982791	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10982846	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11999332	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12342529	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2027929	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2106055	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2188052	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2188053	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2188067	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2418367	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2418393	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3899074	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246911	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979550	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4979551	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4979569	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4997383	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478180	0.90[EUR][1000 genomes]
rs6478181	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6478183	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6478184	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6478185	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7024456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7026805	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7027022	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7029913	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7030481	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7033287	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7046356	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs718019	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7466595	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7466771	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7467026	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7467728	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7468290	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7469165	0.87[EUR][1000 genomes]
rs7469418	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7469817	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7470070	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7855143	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7858000	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs916554	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs916555	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs963115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs969832	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs976499	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1046948	chr9:118185587-118926891	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv916622	chr9:118206309-118952390	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv540207	chr9:118206311-118920304	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv491661	chr9:118206312-118802177	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv831698	chr9:118284259-118446456	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1047164	chr9:118286742-118456851	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6478196	C9orf27	cis	parietal	SCAN
rs6478196	HDHD3	cis	cerebellum	SCAN
rs6478196	DEC1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118358400-118377800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:118376600-118377600	Enhancers	Osteobl	bone
3	chr9:118376600-118377800	Enhancers	NHEK	skin
4	chr9:118376600-118377800	Enhancers	NHLF	lung
5	chr9:118376600-118378200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:118376600-118379000	Enhancers	HSMM	muscle
7	chr9:118376600-118379800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:118376600-118379800	Enhancers	NHDF-Ad	bronchial
9	chr9:118376600-118380000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:118376600-118380000	Enhancers	HMEC	breast
11	chr9:118376800-118377800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:118376800-118379000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:118376800-118379400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:118376800-118379800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:118377000-118377800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:118377000-118379600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr9:118377200-118378200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:118377200-118378200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr9:118377400-118377600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:118377400-118377800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:118377400-118377800	Enhancers	NH-A	brain
22	chr9:118377400-118378200	Flanking Active TSS	A549	lung
23	chr9:118377400-118378200	Flanking Active TSS	Hela-S3	cervix
24	chr9:118377400-118378200	Enhancers	HSMMtube	muscle
25	chr9:118377400-118378400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:118377400-118378800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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