Variant report

Variant	rs4141712
Chromosome Location	chr9:21557406-21557407
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10118880	0.89[EUR][1000 genomes]
rs10738594	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10757225	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10965064	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1545749	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1983811	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4141713	0.92[EUR][1000 genomes]
rs9298816	0.92[EUR][1000 genomes]
rs9298817	0.82[EUR][1000 genomes]
rs9657572	0.97[EUR][1000 genomes]
rs9657607	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs996442	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4141712	LOC554202	cis	cerebellum	SCAN

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	chr9:21554800-21558800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:21554800-21560600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr9:21555000-21558600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:21555200-21558600	Active TSS	Fetal Intestine Small	intestine
9	chr9:21555200-21560000	Active TSS	Hela-S3	cervix
10	chr9:21555200-21560800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:21555400-21558600	Active TSS	Duodenum Mucosa	Duodenum
12	chr9:21555800-21558600	Weak transcription	HSMMtube	muscle
13	chr9:21555800-21560200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:21556200-21558200	Weak transcription	HSMM	muscle
15	chr9:21556200-21558400	Active TSS	Muscle Satellite Cultured Cells	--
16	chr9:21556200-21559200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:21556200-21559200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:21556200-21560000	Active TSS	HMEC	breast
19	chr9:21556200-21560200	Active TSS	NH-A	brain
20	chr9:21556200-21560200	Active TSS	Osteobl	bone
21	chr9:21556200-21560400	Active TSS	NHLF	lung
22	chr9:21556400-21557800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:21556400-21558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:21556400-21558200	Active TSS	NHEK	skin
25	chr9:21556400-21560000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:21556400-21560400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:21556400-21560600	Active TSS	NHDF-Ad	bronchial
28	chr9:21556600-21558000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:21556600-21560200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:21556800-21558000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr9:21556800-21558200	Active TSS	Fetal Intestine Large	intestine
32	chr9:21557000-21558800	Active TSS	Stomach Mucosa	stomach
33	chr9:21557000-21560400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
34	chr9:21557200-21558200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
35	chr9:21557400-21559400	Transcr. at gene 5' and 3'	A549	lung
36	chr9:21557400-21560000	Active TSS	HUVEC	blood vessel

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