Variant report

Variant	rs654422
Chromosome Location	chr9:27181761-27181762
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1178258	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2181031	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs553450	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs558931	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs591831	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs633903	0.81[LWK][hapmap]
rs685434	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv6512	chr9:27155677-27200455	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv892864	chr9:27176554-27296705	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv466335	chr9:27179244-27234029	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv613946	chr9:27179244-27234029	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs654422	ASCL3	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27151000-27229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:27158200-27183600	Weak transcription	Lung	lung
3	chr9:27165400-27198200	Weak transcription	Ovary	ovary
4	chr9:27165400-27219200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:27166000-27183600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:27166200-27192200	Weak transcription	Fetal Stomach	stomach
7	chr9:27166200-27205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:27166200-27229000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:27174800-27183200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:27174800-27183800	Weak transcription	Right Ventricle	heart
11	chr9:27178400-27183600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr9:27178400-27197200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:27179000-27182400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:27179400-27182400	Enhancers	HSMM	muscle
15	chr9:27179400-27184800	Enhancers	NHEK	skin
16	chr9:27179600-27184200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:27179600-27191800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:27179800-27182000	Weak transcription	HSMMtube	muscle
19	chr9:27180000-27183400	Weak transcription	NH-A	brain
20	chr9:27180400-27183600	Weak transcription	Left Ventricle	heart
21	chr9:27180600-27184600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr9:27180800-27182000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:27180800-27182600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:27180800-27184200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:27180800-27191800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:27180800-27230600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:27181000-27184200	Enhancers	HMEC	breast
28	chr9:27181200-27181800	Enhancers	HUVEC	blood vessel
29	chr9:27181400-27183800	Enhancers	Hela-S3	cervix
30	chr9:27181400-27184600	Enhancers	Osteobl	bone
31	chr9:27181600-27181800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:27181600-27182400	Enhancers	Adipose Nuclei	Adipose
33	chr9:27181600-27182400	Enhancers	Brain Germinal Matrix	brain
34	chr9:27181600-27183000	Enhancers	Fetal Lung	lung
35	chr9:27181600-27183200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:27181600-27183600	Weak transcription	NHLF	lung

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