Variant report

Variant	rs3810926
Chromosome Location	chr9:116259900-116259901
allele	C/T
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	chr9:116259879-116260019	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:116259892..116262727-chr9:116263067..116266319,3	MCF-7	breast:
2	chr9:116256606..116259103-chr9:116259265..116261793,2	MCF-7	breast:
3	chr9:116254507..116256265-chr9:116258071..116260770,2	MCF-7	breast:

Variant related genes	Relation type
RGS3	TF binding region
ENSG00000138835	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10981793	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10981815	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12338788	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12347382	0.86[ASN][1000 genomes]
rs12351728	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17525042	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17553698	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2761025	1.00[LWK][hapmap];0.85[MKK][hapmap]
rs34106027	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34142167	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35081798	0.97[EUR][1000 genomes]
rs35120599	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35329679	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747813	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]
rs3761819	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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];1.00[ASN][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];1.00[ASN][1000 genomes]
rs41276809	0.97[EUR][1000 genomes];1.00[ASN][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]
rs41312200	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41316948	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55714377	0.86[ASN][1000 genomes]
rs7042968	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7049221	1.00[CHB][hapmap]
rs72760096	1.00[ASN][1000 genomes]
rs72761906	0.86[ASN][1000 genomes]
rs72761963	0.86[ASN][1000 genomes]
rs72761965	0.86[ASN][1000 genomes]
rs7851937	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7852118	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs7854524	1.00[CHB][hapmap]
rs7855434	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7856689	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7857217	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7864467	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs7864816	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7870142	0.86[ASN][1000 genomes]
rs7870912	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs883025	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs884898	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9785299	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3810926	POLE3	cis	multi-tissue	Pritchard
rs3810926	POLE3	cis	lymphoblastoid	seeQTL
rs3810926	RGS3	cis	Whole Blood	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116227400-116263800	Weak transcription	Colonic Mucosa	Colon
2	chr9:116242000-116263600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:116242000-116266200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:116248600-116261600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:116248800-116261600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:116251000-116263800	Weak transcription	Esophagus	oesophagus
7	chr9:116251200-116263200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:116251600-116283800	Weak transcription	Hela-S3	cervix
9	chr9:116251800-116261600	Weak transcription	HepG2	liver
10	chr9:116252000-116260200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr9:116252400-116273200	Weak transcription	Pancreas	Pancrea
12	chr9:116252600-116262000	Weak transcription	A549	lung
13	chr9:116255400-116264000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:116255400-116264200	Weak transcription	Fetal Kidney	kidney
15	chr9:116255600-116263000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:116255600-116265400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr9:116255600-116266600	Weak transcription	Stomach Mucosa	stomach
18	chr9:116255600-116269400	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:116255600-116275800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr9:116255800-116263800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:116255800-116263800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:116255800-116264800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr9:116256000-116260200	Weak transcription	Placenta	Placenta
24	chr9:116256000-116261800	Weak transcription	Fetal Thymus	thymus
25	chr9:116256000-116261800	Weak transcription	Lung	lung
26	chr9:116256000-116262400	Weak transcription	Right Ventricle	heart
27	chr9:116256000-116264800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:116256200-116261600	Weak transcription	Right Atrium	heart
29	chr9:116256600-116261600	Weak transcription	Fetal Heart	heart
30	chr9:116256800-116263800	Strong transcription	Fetal Intestine Small	intestine
31	chr9:116257000-116262400	Weak transcription	Left Ventricle	heart
32	chr9:116257400-116270800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr9:116257800-116262400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:116257800-116263400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr9:116257800-116263600	Weak transcription	Spleen	Spleen
36	chr9:116258600-116263800	Weak transcription	Fetal Intestine Large	intestine
37	chr9:116259000-116262400	Weak transcription	Fetal Muscle Leg	muscle
38	chr9:116259200-116260000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:116259200-116274000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:116259200-116274200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:116259400-116260800	Strong transcription	Aorta	Aorta
42	chr9:116259600-116260200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr9:116259600-116261800	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr9:116259600-116263800	Strong transcription	Fetal Stomach	stomach
45	chr9:116259800-116263800	Weak transcription	Gastric	stomach

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