Variant report

Variant	rs4979570
Chromosome Location	chr9:118392208-118392209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1006008	0.81[ASN][1000 genomes]
rs10116519	0.82[ASN][1000 genomes]
rs10118599	0.88[EUR][1000 genomes]
rs10759793	0.88[EUR][1000 genomes]
rs10759794	0.89[EUR][1000 genomes]
rs10759810	0.95[EUR][1000 genomes]
rs10817793	0.88[EUR][1000 genomes]
rs10817794	0.89[EUR][1000 genomes]
rs10817803	0.94[EUR][1000 genomes]
rs10817804	0.94[EUR][1000 genomes]
rs10982798	0.89[EUR][1000 genomes]
rs12005078	0.89[EUR][1000 genomes]
rs2040481	0.89[EUR][1000 genomes]
rs2157669	0.89[EUR][1000 genomes]
rs2188057	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2188063	0.89[EUR][1000 genomes]
rs2188064	0.88[EUR][1000 genomes]
rs2418359	0.89[EUR][1000 genomes]
rs2418366	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2418369	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2418393	0.81[ASN][1000 genomes]
rs4246911	0.81[ASN][1000 genomes]
rs4626681	0.87[EUR][1000 genomes]
rs4978645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979552	0.88[EUR][1000 genomes]
rs4979554	0.89[EUR][1000 genomes]
rs4979567	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4979569	0.81[ASN][1000 genomes]
rs6478187	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6478195	0.80[EUR][1000 genomes]
rs6478197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7470070	0.81[ASN][1000 genomes]
rs7470877	0.89[EUR][1000 genomes]
rs7855143	0.81[ASN][1000 genomes]
rs7856039	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856947	0.89[EUR][1000 genomes]
rs7856953	0.89[EUR][1000 genomes]
rs7860973	0.80[EUR][1000 genomes]
rs9299230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969832	0.81[ASN][1000 genomes]
rs976499	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4979570	HDHD3	cis	cerebellum	SCAN
rs4979570	DEC1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118385000-118394800	Weak transcription	Aorta	Aorta
2	chr9:118387800-118395200	Weak transcription	HSMM	muscle
3	chr9:118390000-118393400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:118390400-118392400	Weak transcription	NHLF	lung
5	chr9:118390600-118395000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:118390800-118392400	Weak transcription	Osteobl	bone
7	chr9:118390800-118394800	Weak transcription	NH-A	brain
8	chr9:118390800-118398800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:118391000-118395200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:118391200-118394800	Weak transcription	NHEK	skin
11	chr9:118391800-118392400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:118391800-118393400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:118392000-118392400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:118392000-118393000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:118392200-118392600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:118392200-118392600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr9:118392200-118392600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:118392200-118392600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr9:118392200-118392800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr9:118392200-118392800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr9:118392200-118393000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:118392200-118393000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr9:118392200-118393000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:118392200-118393400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:118392200-118393600	Enhancers	NHDF-Ad	bronchial

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