Variant report

Variant	rs10491564
Chromosome Location	chr9:21556280-21556281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10491563	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10964990	1.00[AFR][1000 genomes]
rs10964991	1.00[AFR][1000 genomes]
rs10964992	1.00[AFR][1000 genomes]
rs12686498	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13294656	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1351077	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs16938465	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16938468	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4585835	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4977727	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4978118	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
2	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10491564	CUL3	trans	lymphoblastoid	RTeQTL
rs10491564	BCLAF1	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21548400-21558200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:21552600-21558600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:21553000-21558600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:21553600-21558000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:21553800-21556800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr9:21553800-21557400	Active TSS	A549	lung
7	chr9:21554200-21556800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:21554800-21558800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:21554800-21560600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr9:21555000-21557400	Flanking Active TSS	HUVEC	blood vessel
11	chr9:21555000-21558600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:21555200-21556400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr9:21555200-21558600	Active TSS	Fetal Intestine Small	intestine
14	chr9:21555200-21560000	Active TSS	Hela-S3	cervix
15	chr9:21555200-21560800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:21555400-21556400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr9:21555400-21556400	Transcr. at gene 5' and 3'	NHEK	skin
18	chr9:21555400-21558600	Active TSS	Duodenum Mucosa	Duodenum
19	chr9:21555800-21556400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr9:21555800-21556400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:21555800-21556600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:21555800-21558600	Weak transcription	HSMMtube	muscle
23	chr9:21555800-21560200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:21556000-21556400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:21556000-21556400	Flanking Active TSS	NHDF-Ad	bronchial
26	chr9:21556200-21556600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:21556200-21556800	Weak transcription	Fetal Intestine Large	intestine
28	chr9:21556200-21557000	Weak transcription	Stomach Mucosa	stomach
29	chr9:21556200-21558200	Weak transcription	HSMM	muscle
30	chr9:21556200-21558400	Active TSS	Muscle Satellite Cultured Cells	--
31	chr9:21556200-21559200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:21556200-21559200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:21556200-21560000	Active TSS	HMEC	breast
34	chr9:21556200-21560200	Active TSS	NH-A	brain
35	chr9:21556200-21560200	Active TSS	Osteobl	bone
36	chr9:21556200-21560400	Active TSS	NHLF	lung

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