Variant report

Variant	rs12352964
Chromosome Location	chr9:72667128-72667129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11141566	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11141672	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11141697	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11142141	0.90[CHB][hapmap]
rs12349576	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1927104	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1927107	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28462281	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2997657	0.90[ASN][1000 genomes]
rs2997665	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015234	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3015237	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015239	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4237238	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237239	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237240	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4367620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744971	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744972	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744979	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744981	0.87[ASN][1000 genomes]
rs6559970	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7035878	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7045153	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs755778	0.91[ASN][1000 genomes]
rs7853094	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7873075	0.90[CHB][hapmap]

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	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12352964	BHLHB9	trans	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72660000-72668400	Weak transcription	HUVEC	blood vessel
2	chr9:72660200-72668200	Weak transcription	Pancreas	Pancrea
3	chr9:72660200-72668400	Weak transcription	Gastric	stomach
4	chr9:72661600-72671600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:72661600-72672000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:72661800-72671600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:72664000-72667400	Enhancers	Colon Smooth Muscle	Colon
8	chr9:72664400-72668400	Weak transcription	Spleen	Spleen
9	chr9:72664600-72667800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:72664800-72667200	Weak transcription	Liver	Liver
11	chr9:72664800-72667400	Weak transcription	Psoas Muscle	Psoas
12	chr9:72664800-72668400	Weak transcription	Esophagus	oesophagus
13	chr9:72664800-72668600	Weak transcription	Brain Germinal Matrix	brain
14	chr9:72664800-72668600	Weak transcription	NH-A	brain
15	chr9:72664800-72670400	Weak transcription	Left Ventricle	heart
16	chr9:72664800-72670400	Weak transcription	Right Ventricle	heart
17	chr9:72665000-72667200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:72665000-72667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:72665000-72667800	Weak transcription	NHEK	skin
20	chr9:72665000-72668000	Enhancers	Rectal Smooth Muscle	rectum
21	chr9:72665000-72668400	Weak transcription	NHDF-Ad	bronchial
22	chr9:72665000-72669800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:72665000-72670200	Weak transcription	Lung	lung
24	chr9:72665200-72667200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:72665200-72667200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:72665200-72667800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:72665200-72668400	Weak transcription	Fetal Muscle Leg	muscle
28	chr9:72665200-72668800	Weak transcription	Osteobl	bone
29	chr9:72665200-72670200	Weak transcription	Fetal Stomach	stomach
30	chr9:72665200-72673600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:72665400-72669600	Weak transcription	Fetal Lung	lung
32	chr9:72665400-72673200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:72666200-72667200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:72666200-72667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:72666200-72667400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:72666200-72667400	Weak transcription	HSMM	muscle
37	chr9:72666200-72667800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr9:72666400-72667400	Weak transcription	Ovary	ovary
39	chr9:72666400-72667800	Weak transcription	Right Atrium	heart
40	chr9:72666400-72667800	Weak transcription	HSMMtube	muscle
41	chr9:72666800-72668000	Enhancers	Stomach Smooth Muscle	stomach
42	chr9:72666800-72670600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr9:72667000-72667200	Enhancers	Adipose Nuclei	Adipose
44	chr9:72667000-72667200	Enhancers	Aorta	Aorta
45	chr9:72667000-72667600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:72667000-72667600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:72667000-72668800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:72667000-72669200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr9:72667000-72669400	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr9:72667000-72669400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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