Variant report

Variant	rs4907308
Chromosome Location	chr2:96927965-96927966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:96923812..96929557-chr2:96929618..96934014,11	K562	blood:
2	chr2:96873130..96877842-chr2:96924423..96928437,5	K562	blood:
3	chr2:96810611..96813061-chr2:96927230..96929575,2	K562	blood:
4	chr2:96911457..96914328-chr2:96926572..96928354,2	MCF-7	breast:
5	chr2:96815199..96817258-chr2:96927223..96929849,2	K562	blood:
6	chr2:96873368..96875940-chr2:96925082..96928161,5	MCF-7	breast:
7	chr2:96927795..96929440-chr2:97175507..97178094,2	MCF-7	breast:
8	chr2:96872598..96876007-chr2:96924059..96928423,13	MCF-7	breast:
9	chr2:96888662..96890849-chr2:96927817..96930448,2	MCF-7	breast:
10	chr2:96802971..96805127-chr2:96925819..96928248,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135956	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000158050	Chromatin interaction
ENSG00000228873	Chromatin interaction
ENSG00000188886	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1044594	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1048675	0.84[AMR][1000 genomes]
rs11903461	0.82[AMR][1000 genomes]
rs17420101	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17479466	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17633463	0.83[AMR][1000 genomes]
rs2276648	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2276649	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2279105	0.85[AMR][1000 genomes]
rs3171927	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3214058	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3214063	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3731930	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4907231	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4907232	0.97[ASN][1000 genomes]
rs4907307	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4907309	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4907310	0.82[AMR][1000 genomes]
rs4907311	0.81[AMR][1000 genomes]
rs56800261	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59966106	0.82[AMR][1000 genomes]
rs59979953	0.81[AMR][1000 genomes]
rs62153033	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62153034	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62153035	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62153039	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62153041	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62153898	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62153900	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62153901	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62153902	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62153905	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62153906	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7562544	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4907308	CIAO1	cis	Whole Blood	GTEx
rs4907308	AC008268.2	cis	Artery Tibial	GTEx
rs4907308	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs4907308	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs4907308	CIAO1	cis	Esophagus Mucosa	GTEx
rs4907308	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs4907308	AC008268.2	cis	lung	GTEx
rs4907308	CIAO1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96914400-96929800	Strong transcription	Fetal Stomach	stomach
2	chr2:96916000-96929400	Strong transcription	Dnd41	blood
3	chr2:96917400-96929600	Strong transcription	Brain Germinal Matrix	brain
4	chr2:96918200-96929400	Weak transcription	Fetal Brain Male	brain
5	chr2:96918200-96929600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:96920200-96928000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr2:96920200-96930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:96921000-96929800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:96921200-96929800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:96921200-96930200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:96921800-96930200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:96922200-96928400	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr2:96922600-96928400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:96923000-96928400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:96923400-96929600	Strong transcription	Fetal Brain Female	brain
16	chr2:96923600-96928400	Genic enhancers	Fetal Intestine Small	intestine
17	chr2:96923800-96928000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:96923800-96928200	Genic enhancers	Spleen	Spleen
19	chr2:96923800-96928200	Enhancers	NHDF-Ad	bronchial
20	chr2:96923800-96928400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:96923800-96928800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:96923800-96929400	Enhancers	Right Atrium	heart
23	chr2:96923800-96930600	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr2:96924000-96928400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:96924000-96929200	Strong transcription	Thymus	Thymus
26	chr2:96924200-96929800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr2:96924400-96930200	Enhancers	Pancreas	Pancrea
28	chr2:96924800-96929800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:96925000-96929800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr2:96925200-96929800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:96925400-96928000	Enhancers	Fetal Intestine Large	intestine
32	chr2:96925600-96928200	Flanking Active TSS	HepG2	liver
33	chr2:96925600-96928400	Enhancers	HMEC	breast
34	chr2:96925800-96928200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:96926200-96928400	Enhancers	Stomach Mucosa	stomach
36	chr2:96926400-96928400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:96926400-96929400	Enhancers	Fetal Heart	heart
38	chr2:96926600-96929400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:96926600-96930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:96926800-96928000	Genic enhancers	GM12878-XiMat	blood
41	chr2:96926800-96928200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:96926800-96928600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr2:96926800-96929400	Weak transcription	Aorta	Aorta
44	chr2:96926800-96930000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:96926800-96930200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:96927000-96928000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:96927000-96928000	Genic enhancers	Hela-S3	cervix
48	chr2:96927000-96928000	Weak transcription	Osteobl	bone
49	chr2:96927000-96928200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:96927000-96928400	Enhancers	Muscle Satellite Cultured Cells	--

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