Variant report

Variant	rs6478142
Chromosome Location	chr9:117924752-117924753
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10120799	0.93[EUR][1000 genomes]
rs10122188	0.93[EUR][1000 genomes]
rs10124924	0.93[EUR][1000 genomes]
rs10125919	0.93[EUR][1000 genomes]
rs10125923	0.93[EUR][1000 genomes]
rs10125938	0.93[EUR][1000 genomes]
rs10465110	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10465131	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10817717	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10817719	0.93[EUR][1000 genomes]
rs10817720	0.93[EUR][1000 genomes]
rs10982548	0.98[ASN][1000 genomes]
rs10982549	1.00[ASN][1000 genomes]
rs10982551	0.98[ASN][1000 genomes]
rs10982560	1.00[ASN][1000 genomes]
rs10982561	0.81[ASN][1000 genomes]
rs10982562	0.83[ASN][1000 genomes]
rs10982563	1.00[ASN][1000 genomes]
rs10982564	1.00[ASN][1000 genomes]
rs10982565	1.00[ASN][1000 genomes]
rs10982566	1.00[ASN][1000 genomes]
rs10982568	1.00[ASN][1000 genomes]
rs10982569	1.00[ASN][1000 genomes]
rs10982570	1.00[ASN][1000 genomes]
rs10982571	1.00[ASN][1000 genomes]
rs10982573	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982574	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982575	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982578	0.88[EUR][1000 genomes]
rs10982580	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982581	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982582	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982583	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982584	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982586	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982587	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10982588	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982589	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982590	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982591	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982592	0.85[EUR][1000 genomes]
rs10982596	0.90[EUR][1000 genomes]
rs10982597	0.90[EUR][1000 genomes]
rs12115360	0.90[EUR][1000 genomes]
rs12115362	0.93[EUR][1000 genomes]
rs12237691	0.98[ASN][1000 genomes]
rs12338815	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338911	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345367	0.82[EUR][1000 genomes]
rs12346640	0.81[EUR][1000 genomes]
rs12347993	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348952	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289510	0.93[EUR][1000 genomes]
rs16932289	1.00[ASN][1000 genomes]
rs4607691	0.93[EUR][1000 genomes]
rs56791225	0.98[ASN][1000 genomes]
rs59205962	0.95[ASN][1000 genomes]
rs60003319	0.95[ASN][1000 genomes]
rs60715510	0.91[EUR][1000 genomes]
rs60760004	0.98[ASN][1000 genomes]
rs6478136	1.00[ASN][1000 genomes]
rs6478138	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478139	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478140	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478143	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6478144	1.00[ASN][1000 genomes]
rs7027235	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027851	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7030384	0.85[EUR][1000 genomes]
rs7031730	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031771	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7048739	0.85[EUR][1000 genomes]
rs7357687	0.82[EUR][1000 genomes]
rs7357688	0.82[EUR][1000 genomes]
rs7847093	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851019	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851086	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851110	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851481	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859387	1.00[ASN][1000 genomes]
rs7862558	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864609	0.95[ASN][1000 genomes]
rs7866441	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9299221	0.82[EUR][1000 genomes]
rs9886849	0.82[EUR][1000 genomes]
rs9886855	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv6681	chr9:117893926-117938609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117920400-117925800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:117920400-117925800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:117920600-117926400	Weak transcription	NHEK	skin
4	chr9:117921400-117926600	Weak transcription	HSMMtube	muscle
5	chr9:117921600-117925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:117921600-117925800	Weak transcription	NHLF	lung
7	chr9:117921600-117926400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:117921600-117926600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:117921600-117926800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:117921800-117926800	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:117922000-117924800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:117922000-117925800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr9:117922000-117944600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:117923000-117924800	Enhancers	Fetal Intestine Small	intestine
15	chr9:117923400-117927600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:117924000-117926400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:117924200-117925800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:117924200-117925800	Weak transcription	NHDF-Ad	bronchial
19	chr9:117924200-117926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:117924400-117924800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:117924600-117926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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