Variant report

Variant	rs6440525
Chromosome Location	chr3:99013185-99013186
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1318850	0.87[EUR][1000 genomes]
rs1383839	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1546695	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1574857	0.87[EUR][1000 genomes]
rs2200017	0.89[EUR][1000 genomes]
rs2341812	0.87[EUR][1000 genomes]
rs2341813	0.89[EUR][1000 genomes]
rs2880156	0.90[EUR][1000 genomes]
rs4426705	0.86[EUR][1000 genomes]
rs4481186	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59089459	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62281919	0.80[EUR][1000 genomes]
rs62281920	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62281921	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62281949	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62283771	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788883	0.81[AMR][1000 genomes]
rs6789067	0.81[AMR][1000 genomes]
rs71620012	0.89[EUR][1000 genomes]
rs73138428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615735	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7622093	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7633383	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7637232	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs974686	0.89[EUR][1000 genomes]
rs9823613	0.86[EUR][1000 genomes]
rs9860091	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530026	chr3:98837320-99340537	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1798220	chr3:98894142-99020463	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1002786	chr3:98944446-99013936	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv818163	chr3:99005053-99015616	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6440525	COL8A1	cis	cerebellum	SCAN
rs6440525	NAPEPLD	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99013000-99013200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:99013000-99013200	Active TSS	H1 Cell Line	embryonic stem cell
3	chr3:99013000-99013200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:99013000-99013200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:99013000-99013200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:99013000-99013200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr3:99013000-99013200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:99013000-99013200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:99013000-99013200	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr3:99013000-99013200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:99013000-99013200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:99013000-99013200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:99013000-99013200	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr3:99013000-99013200	Active TSS	Dnd41	blood
15	chr3:99013000-99013200	Active TSS	NHEK	skin
16	chr3:99013000-99013400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:99013000-99013400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:99013000-99013400	Enhancers	HUVEC	blood vessel
19	chr3:99013000-99013400	Enhancers	Osteobl	bone
20	chr3:99013000-99013600	Enhancers	H9 Cell Line	embryonic stem cell
21	chr3:99013000-99013600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:99013000-99013600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:99013000-99013600	Enhancers	HMEC	breast
24	chr3:99013000-99013600	Enhancers	NHLF	lung
25	chr3:99013000-99013800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:99013000-99014000	Enhancers	Muscle Satellite Cultured Cells	--

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