Variant report

Variant	rs4907307
Chromosome Location	chr2:96925269-96925270
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr2:96874408..96876271-chr2:96925161..96927177,2	K562	blood:
4	chr2:96925245..96927615-chr2:96969806..96971741,2	MCF-7	breast:
5	chr2:96873368..96875940-chr2:96925082..96928161,5	MCF-7	breast:
6	chr2:96872598..96876007-chr2:96924059..96928423,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204685	Chromatin interaction
ENSG00000135956	Chromatin interaction
ENSG00000144028	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000144021	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1044594	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1048675	0.92[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11551400	0.88[YRI][hapmap]
rs11903461	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17420101	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17479466	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2276648	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2276649	0.92[CEU][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2279105	0.92[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2305935	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs3171927	0.81[CEU][hapmap]
rs3214058	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3214063	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3731930	1.00[CEU][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4907231	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4907308	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4907309	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4907310	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4907311	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4907312	0.84[CEU][hapmap]
rs56800261	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57406815	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58328293	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59966106	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59979953	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62153033	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62153034	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62153035	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62153039	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62153041	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62153898	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62153900	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62153901	0.83[AMR][1000 genomes]
rs62153902	0.83[AMR][1000 genomes]
rs62153905	0.81[AMR][1000 genomes]
rs62153906	0.82[AMR][1000 genomes]
rs62153915	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6737429	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs7562544	0.84[CEU][hapmap];0.83[AMR][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
rs4907307	CIAO1	cis	Whole Blood	GTEx
rs4907307	AC008268.2	cis	Whole Blood	GTEx
rs4907307	AC008268.2	cis	Nerve Tibial	GTEx
rs4907307	AC008268.2	cis	Artery Tibial	GTEx
rs4907307	CIAO1	cis	Adipose Subcutaneous	GTEx
rs4907307	AC008268.2	cis	lung	GTEx
rs4907307	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs4907307	CIAO1	cis	Lymphoblastoid	GTEx
rs4907307	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs4907307	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs4907307	CIAO1	cis	lung	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	chr2:96917600-96925600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:96917800-96925600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:96918000-96926000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:96918200-96929400	Weak transcription	Fetal Brain Male	brain
8	chr2:96918200-96929600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:96918400-96925600	Weak transcription	NH-A	brain
10	chr2:96919800-96925800	Weak transcription	Small Intestine	intestine
11	chr2:96920200-96928000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr2:96920200-96930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:96920600-96927400	Weak transcription	Fetal Lung	lung
14	chr2:96920800-96926000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:96920800-96926000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:96920800-96926200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:96921000-96927800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:96921000-96929800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:96921200-96926200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:96921200-96929800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:96921200-96930200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:96921400-96925400	Weak transcription	Fetal Kidney	kidney
23	chr2:96921600-96925800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:96921600-96925800	Weak transcription	NHEK	skin
25	chr2:96921800-96925600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:96921800-96925800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:96921800-96926000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:96921800-96927200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:96921800-96930200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:96922200-96928400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:96922600-96925400	Genic enhancers	Rectal Mucosa Donor 29	rectum
32	chr2:96922600-96927600	Genic enhancers	Fetal Muscle Leg	muscle
33	chr2:96922600-96927800	Enhancers	Left Ventricle	heart
34	chr2:96922600-96927800	Enhancers	Psoas Muscle	Psoas
35	chr2:96922600-96928400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr2:96922800-96927200	Enhancers	Primary hematopoietic stem cells	blood
37	chr2:96923000-96925400	Weak transcription	Gastric	stomach
38	chr2:96923000-96927400	Enhancers	Primary B cells from cord blood	blood
39	chr2:96923000-96928400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr2:96923400-96925400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:96923400-96927400	Genic enhancers	Lung	lung
42	chr2:96923400-96929600	Strong transcription	Fetal Brain Female	brain
43	chr2:96923600-96925400	Genic enhancers	Fetal Intestine Large	intestine
44	chr2:96923600-96925400	Genic enhancers	Stomach Smooth Muscle	stomach
45	chr2:96923600-96925600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:96923600-96925600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:96923600-96926000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:96923600-96926000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:96923600-96926000	Enhancers	Liver	Liver
50	chr2:96923600-96926400	Enhancers	Right Ventricle	heart

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