Variant report

Variant	rs62153901
Chromosome Location	chr2:96983959-96983960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96977549..96980763-chr2:96982097..96985833,3	K562	blood:
2	chr2:96968224..96973301-chr2:96983171..96988936,6	MCF-7	breast:
3	chr2:96969674..96973937-chr2:96983543..96988332,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144028	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1044594	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1048675	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11903461	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17420101	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17479466	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17633463	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276648	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2276649	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2279105	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3171927	1.00[ASN][1000 genomes]
rs3214058	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3214063	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3731930	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3731935	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3731936	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4907231	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907232	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907307	0.83[AMR][1000 genomes]
rs4907308	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4907309	0.84[AMR][1000 genomes]
rs4907310	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4907311	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4907312	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56027554	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56800261	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57406815	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58328293	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59966106	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59979953	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62153033	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153034	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62153035	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62153039	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62153041	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62153898	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62153900	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62153902	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62153905	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62153906	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62153915	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62153923	0.81[AMR][1000 genomes]
rs6755877	0.82[AMR][1000 genomes]
rs7562544	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62153901	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs62153901	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs62153901	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs62153901	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs62153901	AC008268.2	cis	Artery Tibial	GTEx
rs62153901	AC008268.2	cis	lung	GTEx
rs62153901	CIAO1	cis	Esophagus Mucosa	GTEx
rs62153901	CIAO1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96980400-96986400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:96980800-96985200	Enhancers	HepG2	liver
3	chr2:96980800-96986200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr2:96981600-96986800	Weak transcription	Spleen	Spleen
5	chr2:96981800-96986200	Weak transcription	K562	blood
6	chr2:96982000-96984600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr2:96982000-96986400	Weak transcription	Hela-S3	cervix
8	chr2:96982000-96986600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:96982200-96984600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr2:96982200-96984600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:96982200-96984800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:96982200-96985000	Weak transcription	Primary B cells from cord blood	blood
13	chr2:96982200-96985600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:96982200-96986000	Weak transcription	A549	lung
15	chr2:96982200-96986400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:96982200-96986600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:96982200-96986600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:96982200-96986600	Weak transcription	NHLF	lung
19	chr2:96982400-96984800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:96982400-96984800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:96982400-96986000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:96982400-96986400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:96982400-96986400	Weak transcription	Adipose Nuclei	Adipose
24	chr2:96982400-96986600	Weak transcription	HSMM	muscle
25	chr2:96982600-96984800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:96982600-96985200	Weak transcription	Fetal Thymus	thymus
27	chr2:96982600-96985600	Weak transcription	Primary T cells from cord blood	blood
28	chr2:96982600-96986000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:96982600-96986600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:96982600-96986600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:96982600-96986600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:96983000-96984400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:96983000-96984800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:96983000-96984800	Weak transcription	Dnd41	blood
35	chr2:96983200-96984600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:96983600-96984400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:96983600-96984400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr2:96983600-96984400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:96983600-96984600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:96983600-96984600	Weak transcription	GM12878-XiMat	blood
41	chr2:96983600-96986200	Weak transcription	NHDF-Ad	bronchial
42	chr2:96983800-96984000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr2:96983800-96984400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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