Variant report

Variant	rs59979953
Chromosome Location	chr2:97014447-97014448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97013257..97015542-chr2:97017707..97021089,3	MCF-7	breast:
2	chr2:96965129..96966663-chr2:97013515..97015063,2	K562	blood:
3	chr2:97005124..97008505-chr2:97011571..97014972,4	K562	blood:
4	chr2:97000363..97004034-chr2:97006939..97016132,12	K562	blood:
5	chr2:97011149..97012847-chr2:97013394..97016096,2	K562	blood:

Variant related genes	Relation type
ENSG00000121152	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1044594	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1048675	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11903461	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17420101	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17479466	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17633463	0.83[AMR][1000 genomes]
rs2085842	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2276648	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276649	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279105	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2305935	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3214058	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3214063	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731930	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4907231	0.85[AMR][1000 genomes]
rs4907233	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4907307	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4907308	0.81[AMR][1000 genomes]
rs4907309	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907310	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4907311	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56221936	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56800261	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57406815	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58328293	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59966106	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62153033	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62153034	0.83[AMR][1000 genomes]
rs62153035	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62153039	0.84[AMR][1000 genomes]
rs62153041	0.84[AMR][1000 genomes]
rs62153898	0.85[AMR][1000 genomes]
rs62153900	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62153901	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62153902	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62153905	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62153906	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153915	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6737429	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7562544	0.88[AMR][1000 genomes];0.86[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	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs59979953	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs59979953	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs59979953	AC008268.2	cis	Artery Tibial	GTEx
rs59979953	AC008268.2	cis	lung	GTEx
rs59979953	AC008268.2	cis	Nerve Tibial	GTEx
rs59979953	AC008268.2	cis	Artery Aorta	GTEx
rs59979953	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs59979953	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs59979953	CIAO1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97001800-97016400	Weak transcription	Spleen	Spleen
2	chr2:97002000-97036000	Weak transcription	Gastric	stomach
3	chr2:97002200-97018800	Weak transcription	Right Atrium	heart
4	chr2:97002200-97037600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:97002400-97016200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:97002400-97018800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:97002600-97017400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:97002600-97031600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:97002800-97015400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:97002800-97018800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:97002800-97040000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:97003000-97018400	Weak transcription	Fetal Heart	heart
13	chr2:97003200-97031400	Weak transcription	Primary B cells from cord blood	blood
14	chr2:97004000-97040400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:97004200-97040400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:97005000-97018800	Strong transcription	Fetal Thymus	thymus
17	chr2:97006200-97041000	Strong transcription	Dnd41	blood
18	chr2:97006600-97040200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:97006600-97040400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:97006800-97018000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:97006800-97040400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr2:97006800-97040600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:97006800-97040800	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:97007000-97040600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:97007200-97018200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr2:97007200-97023000	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr2:97007200-97023400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:97007200-97024000	Strong transcription	Fetal Stomach	stomach
29	chr2:97007200-97040000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:97007200-97040200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:97007200-97040400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:97007200-97041600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:97007400-97020400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:97007400-97023200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr2:97007400-97023600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:97007400-97040200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:97007400-97040400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:97007400-97040600	Strong transcription	Thymus	Thymus
39	chr2:97007600-97016200	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:97008400-97015600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:97008400-97015600	Weak transcription	Brain Germinal Matrix	brain
42	chr2:97008400-97015600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:97008400-97015600	Weak transcription	Fetal Intestine Large	intestine
44	chr2:97008400-97018400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:97008400-97018400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:97008400-97018800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:97008400-97022800	Strong transcription	HepG2	liver
48	chr2:97008400-97033600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:97010200-97014800	Weak transcription	HUVEC	blood vessel
50	chr2:97010400-97015200	Weak transcription	Osteobl	bone

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