Variant report

Variant	rs3747813
Chromosome Location	chr9:116327460-116327461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116035314..116038256-chr9:116326581..116329349,2	K562	blood:
2	chr9:116172469..116174359-chr9:116325229..116328003,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf43-6	chr9:116327337-116327640	NONHSAT134352
2	lnc-C9orf43-6	chr9:116327337-116327640	NONHSAT134351

Variant related genes	Relation type
ENSG00000176386	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000157653	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10981793	1.00[CHB][hapmap]
rs10981815	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs10981830	0.86[ASN][1000 genomes]
rs12338788	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12351728	1.00[CHB][hapmap]
rs17525042	0.97[EUR][1000 genomes]
rs17553698	0.97[EUR][1000 genomes]
rs2761025	1.00[LWK][hapmap];0.85[MKK][hapmap]
rs34106027	0.97[EUR][1000 genomes]
rs34142167	0.97[EUR][1000 genomes]
rs35081798	0.97[EUR][1000 genomes]
rs35120599	0.97[EUR][1000 genomes]
rs35329679	0.97[EUR][1000 genomes]
rs3761819	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3810925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs3810926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3827674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs41276809	0.97[EUR][1000 genomes]
rs41276823	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41306506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41312200	1.00[EUR][1000 genomes]
rs41316948	1.00[EUR][1000 genomes]
rs7040635	1.00[ASN][1000 genomes]
rs7042968	1.00[CHB][hapmap]
rs7049221	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72761999	1.00[ASN][1000 genomes]
rs72763841	1.00[ASN][1000 genomes]
rs7851937	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7852118	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7854524	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7855434	1.00[CHB][hapmap]
rs7856689	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7857217	1.00[CHB][hapmap]
rs7864467	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7864816	1.00[CHB][hapmap]
rs7870912	1.00[CHB][hapmap]
rs883025	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs884898	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs9785299	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3747813	POLE3	cis	lymphoblastoid	seeQTL
rs3747813	RGS3	cis	Whole Blood	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116311600-116331600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr9:116323200-116328000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr9:116323200-116334800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:116323200-116339000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:116323400-116336200	Weak transcription	Primary T cells from cord blood	blood
6	chr9:116323400-116339400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:116324000-116332800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:116325200-116328400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr9:116325800-116339800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:116326200-116339600	Weak transcription	HUVEC	blood vessel
11	chr9:116326400-116327600	Enhancers	Gastric	stomach
12	chr9:116326400-116328400	Weak transcription	Small Intestine	intestine
13	chr9:116326600-116327600	Bivalent Enhancer	Fetal Brain Male	brain
14	chr9:116326600-116327600	Flanking Active TSS	Osteobl	bone
15	chr9:116326600-116327800	Enhancers	Fetal Thymus	thymus
16	chr9:116326600-116327800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr9:116326600-116328600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr9:116326600-116329000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr9:116326600-116331000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr9:116326600-116332400	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr9:116326800-116327600	Enhancers	Primary hematopoietic stem cells	blood
22	chr9:116326800-116327600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:116326800-116327800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:116326800-116327800	Flanking Active TSS	Brain Germinal Matrix	brain
25	chr9:116326800-116327800	Flanking Active TSS	HSMM	muscle
26	chr9:116326800-116328000	Genic enhancers	Spleen	Spleen
27	chr9:116326800-116328000	Flanking Active TSS	NHLF	lung
28	chr9:116326800-116328200	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr9:116326800-116328600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:116326800-116328600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr9:116326800-116328600	Flanking Active TSS	Rectal Smooth Muscle	rectum
32	chr9:116326800-116328800	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr9:116326800-116328800	Flanking Active TSS	Fetal Lung	lung
34	chr9:116326800-116329000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:116326800-116329200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr9:116326800-116329400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:116326800-116329400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:116326800-116329400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr9:116327000-116327600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr9:116327000-116327600	Enhancers	Primary B cells from cord blood	blood
41	chr9:116327000-116327600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:116327000-116327600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:116327000-116327600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
44	chr9:116327000-116327600	Flanking Active TSS	HMEC	breast
45	chr9:116327000-116327600	Flanking Active TSS	NHDF-Ad	bronchial
46	chr9:116327000-116327800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr9:116327000-116327800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr9:116327000-116327800	Flanking Active TSS	Fetal Heart	heart
49	chr9:116327000-116327800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr9:116327000-116328000	Active TSS	ES-I3 Cell Line	embryonic stem cell

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