Variant report

Variant	rs62153033
Chromosome Location	chr2:96934504-96934505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:96934177-96934726	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:96934210-96935366	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:96934193-96935243	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:96934105-96935435	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:96934151-96935362	K562	blood:	n/a	n/a
6	POLR2A	chr2:96934498-96934520	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:96929992..96934856-chr2:96999935..97004454,8	K562	blood:
2	chr2:96871739..96877156-chr2:96928674..96935050,17	K562	blood:
3	chr2:96868913..96876440-chr2:96928017..96934530,23	K562	blood:
4	chr2:96932066..96934505-chr2:97010263..97012552,2	MCF-7	breast:
5	chr2:96928652..96934635-chr2:96966746..96973769,11	K562	blood:
6	chr2:96934413..96937230-chr2:96969465..96972171,2	MCF-7	breast:
7	chr2:96930148..96938607-chr2:96966008..96973188,21	MCF-7	breast:
8	chr2:96871572..96876906-chr2:96928916..96935631,15	MCF-7	breast:
9	chr2:96929774..96935946-chr2:96940519..96946631,7	K562	blood:
10	chr2:96930650..96934516-chr2:96954888..96957639,4	MCF-7	breast:
11	chr2:96862732..96864612-chr2:96933173..96934680,2	K562	blood:

No data

Variant related genes	Relation type
TMEM127	TF binding region
ENSG00000144028	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000121152	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1044594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1048675	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11903461	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17420101	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17479466	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276648	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276649	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279105	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3214058	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3214063	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731930	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4907231	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4907307	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4907308	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4907309	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4907310	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4907311	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56800261	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57406815	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58328293	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59966106	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59979953	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62153034	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62153035	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62153039	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62153041	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62153898	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62153900	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62153901	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153902	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153905	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62153906	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62153915	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7562544	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs62153033	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs62153033	CIAO1	cis	Adipose Subcutaneous	GTEx
rs62153033	AC008268.2	cis	lung	GTEx
rs62153033	CIAO1	cis	Artery Aorta	GTEx
rs62153033	AC008268.2	cis	Artery Tibial	GTEx
rs62153033	CIAO1	cis	Whole Blood	GTEx
rs62153033	AC008268.2	cis	Nerve Tibial	GTEx
rs62153033	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs62153033	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs62153033	CIAO1	cis	lung	GTEx
rs62153033	AC008268.2	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96932600-96941600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:96932800-96934800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:96932800-96970400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:96933200-96935200	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr2:96933200-96938200	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr2:96933200-96970200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:96933200-96970400	Weak transcription	Right Atrium	heart
8	chr2:96933400-96934600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:96933400-96934600	Genic enhancers	Osteobl	bone
10	chr2:96933400-96935000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:96933400-96935000	Strong transcription	HUVEC	blood vessel
12	chr2:96933400-96935200	Strong transcription	Brain Cingulate Gyrus	brain
13	chr2:96933400-96935400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:96933400-96935400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:96933400-96935400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:96933400-96935400	Strong transcription	Primary hematopoietic stem cells	blood
17	chr2:96933400-96935600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:96933400-96935600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:96933400-96935600	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr2:96933400-96936000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:96933400-96938000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:96933400-96938200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr2:96933400-96941000	Strong transcription	NHEK	skin
24	chr2:96933400-96956800	Strong transcription	Placenta	Placenta
25	chr2:96933400-96957400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:96933400-96968800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:96933400-96969000	Strong transcription	Left Ventricle	heart
28	chr2:96933400-96969200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr2:96933400-96969400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:96933400-96969400	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr2:96933400-96970200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:96933400-96970200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:96933400-96970200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr2:96933400-96970200	Strong transcription	Fetal Lung	lung
35	chr2:96933400-96970200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr2:96933600-96935000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:96933600-96935200	Strong transcription	Fetal Kidney	kidney
38	chr2:96933600-96935200	Strong transcription	Rectal Smooth Muscle	rectum
39	chr2:96933600-96935200	Strong transcription	NH-A	brain
40	chr2:96933600-96935400	Strong transcription	Esophagus	oesophagus
41	chr2:96933600-96935400	Strong transcription	Gastric	stomach
42	chr2:96933600-96935400	Strong transcription	Pancreas	Pancrea
43	chr2:96933600-96935400	Strong transcription	Small Intestine	intestine
44	chr2:96933600-96935400	Strong transcription	Thymus	Thymus
45	chr2:96933600-96935400	Strong transcription	Spleen	Spleen
46	chr2:96933600-96935400	Strong transcription	A549	lung
47	chr2:96933600-96935400	Strong transcription	K562	blood
48	chr2:96933600-96935600	Strong transcription	Brain Hippocampus Middle	brain
49	chr2:96933600-96935600	Strong transcription	Fetal Brain Female	brain
50	chr2:96933600-96935600	Strong transcription	Skeletal Muscle Male	skeletal muscle

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