Variant report

Variant	rs59966106
Chromosome Location	chr2:96999086-96999087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:96998602-96999629	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr2:96999038-96999917	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96968671..96973165-chr2:96996066..97004511,14	MCF-7	breast:
2	chr2:96994464..96999026-chr2:96999064..97001016,4	MCF-7	breast:
3	chr2:96970642..96973351-chr2:96997062..96999572,3	K562	blood:

Variant related genes	Relation type
NCAPH	TF binding region
ENSG00000144028	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1044594	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1048675	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11903461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17420101	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17479466	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17633463	0.80[EUR][1000 genomes]
rs2085842	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2276648	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276649	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279105	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2305935	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3214058	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3214063	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731930	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4907231	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4907233	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4907307	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4907308	0.82[AMR][1000 genomes]
rs4907309	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4907310	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4907311	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56221936	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56800261	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57406815	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58328293	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59979953	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62153033	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62153034	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62153035	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62153039	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62153041	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153898	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153900	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62153901	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62153902	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62153905	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62153906	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62153915	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6737429	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7562544	0.88[AMR][1000 genomes];0.90[EUR][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs59966106	CIAO1	cis	Whole Blood	GTEx
rs59966106	CIAO1	cis	Adipose Subcutaneous	GTEx
rs59966106	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs59966106	AC008268.2	cis	Whole Blood	GTEx
rs59966106	AC008268.2	cis	Artery Aorta	GTEx
rs59966106	CIAO1	cis	lung	GTEx
rs59966106	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs59966106	AC008268.2	cis	Nerve Tibial	GTEx
rs59966106	AC008268.2	cis	Muscle Skeletal	GTEx
rs59966106	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs59966106	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs59966106	AC008268.2	cis	lung	GTEx
rs59966106	AC008268.2	cis	Artery Tibial	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96991600-97000400	Weak transcription	Brain Substantia Nigra	brain
2	chr2:96991600-97000400	Weak transcription	Lung	lung
3	chr2:96991800-97000400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:96991800-97000400	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:96991800-97000400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:96991800-97000400	Weak transcription	Fetal Kidney	kidney
7	chr2:96991800-97000400	Weak transcription	Right Atrium	heart
8	chr2:96991800-97000800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:96991800-97000800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:96992200-97000400	Weak transcription	Primary B cells from cord blood	blood
11	chr2:96992200-97000400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:96992200-97000400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:96992200-97000400	Weak transcription	Pancreas	Pancrea
14	chr2:96992200-97000600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:96992400-96999600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:96992400-97000400	Weak transcription	Primary T cells from cord blood	blood
17	chr2:96992400-97000600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:96992400-97000600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:96992600-96999600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:96992600-97000400	Weak transcription	Esophagus	oesophagus
21	chr2:96992600-97000400	Weak transcription	Fetal Intestine Small	intestine
22	chr2:96992600-97000600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:96992600-97000600	Weak transcription	Right Ventricle	heart
24	chr2:96992600-97000800	Weak transcription	Spleen	Spleen
25	chr2:96992800-97000200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:96992800-97000400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:96992800-97000400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:96992800-97000400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:96993400-97000400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:96993600-97000800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:96993800-97000600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:96994000-96999600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:96994000-97000600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:96994000-97000600	Weak transcription	Fetal Brain Female	brain
35	chr2:96994000-97000800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:96994200-96999600	Weak transcription	GM12878-XiMat	blood
37	chr2:96994200-97000400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:96994200-97000600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:96994400-96999600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr2:96994400-96999600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:96994400-96999800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:96994400-97000400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:96994400-97000400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:96994400-97000400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:96994600-97000400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:96994600-97000400	Weak transcription	Brain Germinal Matrix	brain
47	chr2:96994600-97000400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:96994600-97000400	Weak transcription	Fetal Thymus	thymus
49	chr2:96994600-97000600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:96994800-97000200	Weak transcription	Fetal Muscle Leg	muscle

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