Variant report

Variant	rs10865997
Chromosome Location	chr3:56600531-56600532
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	chr3:56600094-56600696	K562	blood:	n/a	n/a

Variant related genes	Relation type
CCDC66	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11130525	0.81[MEX][hapmap]
rs12486047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496217	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12631156	0.84[AMR][1000 genomes]
rs1316647	0.87[YRI][hapmap]
rs13317989	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs1388256	0.81[MEX][hapmap]
rs2291498	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs282524	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282525	0.81[MEX][hapmap]
rs282526	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282530	0.81[MEX][hapmap]
rs282532	0.84[AMR][1000 genomes]
rs282533	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs282534	0.82[AMR][1000 genomes]
rs282537	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs282538	0.84[AMR][1000 genomes]
rs282539	0.82[AMR][1000 genomes]
rs282543	0.84[AMR][1000 genomes]
rs35349208	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3732505	0.81[MEX][hapmap]
rs3732513	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681726	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs4682001	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs4974218	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974222	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974223	0.81[AMR][1000 genomes]
rs55810735	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66873962	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6767903	0.84[YRI][hapmap]
rs6769055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6799711	0.88[AFR][1000 genomes]
rs7612464	0.81[MEX][hapmap]
rs7628343	0.81[AMR][1000 genomes]
rs7639731	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7640995	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7641898	0.91[YRI][hapmap]
rs873840	0.87[YRI][hapmap]
rs9311609	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs953540	0.87[YRI][hapmap]
rs955248	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9822876	0.88[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9823685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9834064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9847362	0.82[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.87[YRI][hapmap]
rs9867302	0.87[ASW][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.91[YRI][hapmap]
rs9872059	0.81[MEX][hapmap]
rs9873754	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9881152	0.81[AMR][1000 genomes]
rs9985317	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10865997	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs10865997	C3orf63	cis	cerebellum	SCAN
rs10865997	FLNB	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:56592400-56601200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:56592400-56601400	Weak transcription	Left Ventricle	heart
5	chr3:56592400-56601800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:56592400-56601800	Weak transcription	Lung	lung
7	chr3:56592400-56602000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
9	chr3:56592400-56602800	Weak transcription	Gastric	stomach
10	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
11	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
12	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
13	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
15	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
16	chr3:56592600-56601000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:56592600-56601000	Weak transcription	HSMMtube	muscle
18	chr3:56592600-56601800	Weak transcription	Aorta	Aorta
19	chr3:56592600-56602200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:56592600-56602200	Weak transcription	Brain Germinal Matrix	brain
21	chr3:56592600-56602200	Weak transcription	Fetal Brain Male	brain
22	chr3:56592600-56603000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:56592600-56603800	Weak transcription	Stomach Mucosa	stomach
24	chr3:56592800-56602000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:56592800-56602000	Weak transcription	Brain Angular Gyrus	brain
26	chr3:56592800-56602000	Weak transcription	A549	lung
27	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
29	chr3:56593000-56602200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:56593000-56603000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:56593000-56607800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:56593000-56610000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:56593200-56600800	Weak transcription	HepG2	liver
34	chr3:56593200-56602000	Weak transcription	Brain Substantia Nigra	brain
35	chr3:56593200-56608000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:56593200-56609000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:56593200-56609600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:56593400-56602400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:56593400-56607600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:56593400-56608600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:56593600-56609800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:56594000-56603000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:56594200-56602000	Strong transcription	HUVEC	blood vessel
45	chr3:56594200-56608000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:56594400-56609400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:56594800-56604000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr3:56594800-56609000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:56595400-56602000	Weak transcription	Brain Anterior Caudate	brain

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