Variant report

Variant	rs4907309
Chromosome Location	chr2:96936254-96936255
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:96936089-96936265	IMR90	lung:	n/a	n/a
2	POLR2A	chr2:96935909-96936519	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:96935786..96937903-chr2:96948870..96951408,2	MCF-7	breast:
2	chr2:96934413..96937230-chr2:96969465..96972171,2	MCF-7	breast:
3	chr2:96930148..96938607-chr2:96966008..96973188,21	MCF-7	breast:
4	chr2:96935272..96937348-chr2:96947447..96949383,2	K562	blood:
5	chr2:96934617..96938002-chr2:96987663..96991573,3	K562	blood:
6	chr2:96935062..96937810-chr2:97000654..97003812,3	MCF-7	breast:
7	chr2:96934609..96937384-chr2:96952296..96954901,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM127	TF binding region
ENSG00000198885	Chromatin interaction
ENSG00000121152	Chromatin interaction
ENSG00000144028	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs1044594	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048675	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11903461	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17420101	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17479466	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276648	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276649	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279105	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3214058	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3214063	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3731930	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907231	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4907307	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4907308	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4907310	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4907311	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56800261	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57406815	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58328293	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59966106	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59979953	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62153033	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62153034	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62153035	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62153039	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62153041	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62153898	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62153900	0.84[AMR][1000 genomes]
rs62153901	0.84[AMR][1000 genomes]
rs62153902	0.84[AMR][1000 genomes]
rs62153905	0.82[AMR][1000 genomes]
rs62153906	0.83[AMR][1000 genomes]
rs62153915	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7562544	0.84[AMR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4907309	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs4907309	CIAO1	cis	Whole Blood	GTEx
rs4907309	AC008268.2	cis	Artery Tibial	GTEx
rs4907309	CIAO1	cis	lung	GTEx
rs4907309	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs4907309	CIAO1	cis	Artery Aorta	GTEx
rs4907309	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs4907309	CIAO1	cis	Adipose Subcutaneous	GTEx
rs4907309	AC008268.2	cis	Nerve Tibial	GTEx
rs4907309	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4907309	AC008268.2	cis	lung	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	chr2:96932800-96970400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:96933200-96938200	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr2:96933200-96970200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:96933200-96970400	Weak transcription	Right Atrium	heart
6	chr2:96933400-96938000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:96933400-96938200	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr2:96933400-96941000	Strong transcription	NHEK	skin
9	chr2:96933400-96956800	Strong transcription	Placenta	Placenta
10	chr2:96933400-96957400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:96933400-96968800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:96933400-96969000	Strong transcription	Left Ventricle	heart
13	chr2:96933400-96969200	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr2:96933400-96969400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:96933400-96969400	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr2:96933400-96970200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:96933400-96970200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:96933400-96970200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:96933400-96970200	Strong transcription	Fetal Lung	lung
20	chr2:96933400-96970200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:96933600-96936800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:96933600-96936800	Weak transcription	Psoas Muscle	Psoas
23	chr2:96933600-96937200	Strong transcription	Right Ventricle	heart
24	chr2:96933600-96938000	Strong transcription	Brain Substantia Nigra	brain
25	chr2:96933600-96938400	Strong transcription	HSMMtube	muscle
26	chr2:96933600-96938800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:96933600-96938800	Strong transcription	Colon Smooth Muscle	Colon
28	chr2:96933600-96939600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:96933600-96943000	Weak transcription	Fetal Heart	heart
30	chr2:96933600-96960200	Strong transcription	Liver	Liver
31	chr2:96933600-96965800	Strong transcription	Lung	lung
32	chr2:96933600-96966800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:96933600-96966800	Strong transcription	Brain Germinal Matrix	brain
34	chr2:96933600-96967200	Strong transcription	Brain Angular Gyrus	brain
35	chr2:96933600-96969400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:96933600-96969400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:96933600-96969400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr2:96933600-96969600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr2:96933600-96969600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr2:96933600-96969800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:96933600-96969800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:96933600-96969800	Strong transcription	Fetal Intestine Small	intestine
43	chr2:96933600-96969800	Strong transcription	Fetal Stomach	stomach
44	chr2:96933600-96969800	Strong transcription	Hela-S3	cervix
45	chr2:96933600-96970000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:96933600-96970000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:96933600-96970000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:96933600-96970200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:96933600-96970200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:96933600-96970200	Strong transcription	Fetal Muscle Leg	muscle

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