Variant report

Variant	rs14059
Chromosome Location	chr9:7799606-7799607
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70408470..70409240-chr9:7799247..7799915,2	NB4	blood:
2	chr9:7785236..7788053-chr9:7798343..7800585,2	K562	blood:
3	chr9:7764096..7766786-chr9:7797842..7799916,2	MCF-7	breast:
4	chr9:7785236..7787094-chr9:7798343..7800559,2	K562	blood:
5	chr17:56709050..56710030-chr9:7799215..7799951,2	NB4	blood:
6	chr15:59981502..59982267-chr9:7799535..7800195,2	NB4	blood:
7	chr15:25414756..25415321-chr9:7799310..7799908,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000270814	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000140299	Chromatin interaction
ENSG00000273056	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1127430	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4742411	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72697241	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72697245	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72697246	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033077	chr9:7358832-7990735	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv539977	chr9:7358832-7990735	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv613266	chr9:7588854-7901308	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv995116	chr9:7682729-8065192	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv892213	chr9:7770942-7856992	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv892214	chr9:7774180-7822486	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs14059	GLDC	cis	parietal	SCAN
rs14059	C9orf123	cis	cerebellum	SCAN
rs14059	ENAM	trans	parietal	SCAN
rs14059	C9orf123	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:7798200-7800400	Active TSS	K562	blood
2	chr9:7798400-7799800	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr9:7798400-7799800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr9:7798400-7800000	Active TSS	Stomach Smooth Muscle	stomach
5	chr9:7798400-7800000	Active TSS	HSMMtube	muscle
6	chr9:7798400-7800200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:7798400-7800200	Active TSS	Psoas Muscle	Psoas
8	chr9:7798600-7799800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr9:7798600-7799800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr9:7798600-7800000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:7798600-7800000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:7798600-7800000	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr9:7798600-7800200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:7798600-7800200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr9:7798600-7800200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:7798600-7800200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:7798600-7800200	Active TSS	Fetal Kidney	kidney
18	chr9:7798600-7800200	Active TSS	NHLF	lung
19	chr9:7798600-7800400	Active TSS	Thymus	Thymus
20	chr9:7798800-7799800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr9:7798800-7799800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr9:7798800-7799800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:7798800-7799800	Active TSS	Esophagus	oesophagus
24	chr9:7798800-7799800	Active TSS	Placenta Amnion	Placenta Amnion
25	chr9:7798800-7800000	Active TSS	H9 Cell Line	embryonic stem cell
26	chr9:7798800-7800000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:7798800-7800000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:7798800-7800000	Active TSS	Colonic Mucosa	Colon
29	chr9:7798800-7800000	Active TSS	Lung	lung
30	chr9:7798800-7800000	Active TSS	Ovary	ovary
31	chr9:7798800-7800200	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr9:7798800-7800200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:7798800-7800200	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr9:7798800-7800200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:7798800-7800200	Active TSS	Aorta	Aorta
36	chr9:7798800-7800200	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr9:7798800-7800200	Active TSS	Fetal Muscle Trunk	muscle
38	chr9:7798800-7800200	Active TSS	Right Atrium	heart
39	chr9:7798800-7800200	Active TSS	Right Ventricle	heart
40	chr9:7799000-7799800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:7799000-7799800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr9:7799000-7799800	Active TSS	Fetal Brain Male	brain
43	chr9:7799000-7799800	Active TSS	Gastric	stomach
44	chr9:7799000-7800000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr9:7799000-7800000	Active TSS	Fetal Intestine Large	intestine
46	chr9:7799000-7800000	Active TSS	Pancreas	Pancrea
47	chr9:7799000-7800000	Active TSS	Small Intestine	intestine
48	chr9:7799000-7800000	Active TSS	Hela-S3	cervix
49	chr9:7799000-7800000	Active TSS	HepG2	liver
50	chr9:7799000-7800200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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