Variant report

Variant	rs11718982
Chromosome Location	chr3:49132554-49132555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:32)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49132132-49132657	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:49130133-49132598	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:49130077-49133607	HepG2	liver:	n/a	n/a
4	MTA3	chr3:49131273-49132583	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:49130196-49132560	HL-60	blood:	n/a	n/a
6	POLR2A	chr3:49130088-49132647	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr3:49129916-49132662	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:49132459-49132580	ProgFib	skin:	n/a	n/a
9	POLR2A	chr3:49131201-49132559	SK-N-SH	brain:	n/a	n/a

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49131901..49134800-chr6:27804680..27807035,2	K562	blood:
2	chr3:49131855..49133728-chr3:49150296..49151812,2	K562	blood:
3	chr3:49083838..49085438-chr3:49131766..49133657,2	K562	blood:
4	chr3:48699555..48701541-chr3:49130676..49133286,2	K562	blood:
5	chr3:49128910..49133326-chr3:49168969..49172072,7	MCF-7	breast:
6	chr3:49128213..49133667-chr3:49140039..49144982,11	MCF-7	breast:
7	chr3:49128926..49138937-chr3:49145476..49160975,31	K562	blood:
8	chr3:49131116..49132928-chr3:49448988..49450506,2	MCF-7	breast:
9	chr3:49043476..49046691-chr3:49130841..49133756,3	K562	blood:
10	chr3:49130978..49133613-chr3:49137310..49139197,3	MCF-7	breast:
11	chr3:49130002..49134881-chr3:49145556..49149434,6	K562	blood:
12	chr3:49025745..49029382-chr3:49129931..49133067,7	MCF-7	breast:
13	chr3:49129916..49132990-chr3:49447157..49451022,6	K562	blood:
14	chr3:48282372..48284186-chr3:49130575..49132684,2	K562	blood:
15	chr3:49130342..49133374-chr3:49140037..49144249,8	K562	blood:
16	chr3:49050440..49054790-chr3:49130798..49133846,4	MCF-7	breast:
17	chr3:49129847..49133782-chr3:49155056..49162049,12	MCF-7	breast:
18	chr3:49062154..49067981-chr3:49128951..49132856,8	K562	blood:
19	chr3:49055445..49060745-chr3:49128874..49135153,17	MCF-7	breast:
20	chr3:49130473..49134563-chr3:49139987..49143694,13	MCF-7	breast:
21	chr3:49052218..49068794-chr3:49126865..49133927,44	K562	blood:
22	chr3:49131736..49133437-chr3:49134322..49137083,2	MCF-7	breast:
23	chr3:49065295..49067964-chr3:49130021..49133372,4	MCF-7	breast:
24	chr3:49054288..49061452-chr3:49128946..49133927,24	K562	blood:
25	chr3:49131867..49132614-chr6:41040877..41041392,2	Hela-S3	cervix:
26	chr3:49131454..49133143-chr3:49466292..49468330,2	K562	blood:
27	chr3:49130643..49132910-chr3:49449200..49450809,2	MCF-7	breast:
28	chr3:49130019..49133719-chr3:49139545..49142279,6	K562	blood:
29	chr3:49043481..49046136-chr3:49130216..49133089,2	K562	blood:
30	chr3:49056708..49059801-chr3:49129963..49133658,5	MCF-7	breast:
31	chr3:49131330..49133492-chr3:49146918..49149870,2	MCF-7	breast:
32	chr3:49062784..49068653-chr3:49129538..49133266,11	MCF-7	breast:

No data

Variant related genes	Relation type
QRICH1	TF binding region
ENSG00000184348	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000164048	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000178467	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000145029	Chromatin interaction
ENSG00000223343	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000199032	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10049462	0.81[EUR][1000 genomes]
rs10154895	0.89[EUR][1000 genomes]
rs11552724	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11706052	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11706189	0.88[EUR][1000 genomes]
rs11708022	0.85[AMR][1000 genomes]
rs11709092	0.81[AMR][1000 genomes]
rs11709246	0.85[AMR][1000 genomes]
rs11710247	0.88[EUR][1000 genomes]
rs11712006	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11713297	0.88[EUR][1000 genomes]
rs11713694	0.85[AMR][1000 genomes]
rs11716614	0.88[AMR][1000 genomes]
rs11719220	0.88[EUR][1000 genomes]
rs11719457	0.89[AMR][1000 genomes]
rs11720460	0.86[EUR][1000 genomes]
rs12715434	0.86[EUR][1000 genomes]
rs13068038	0.86[EUR][1000 genomes]
rs13072554	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13073997	0.85[AMR][1000 genomes]
rs13074318	0.85[AMR][1000 genomes]
rs13077498	0.81[EUR][1000 genomes]
rs13080725	1.00[AMR][1000 genomes]
rs13086240	0.92[AMR][1000 genomes]
rs13087930	0.85[AMR][1000 genomes]
rs13090839	0.89[AMR][1000 genomes]
rs13094900	0.82[AMR][1000 genomes]
rs13096406	0.88[EUR][1000 genomes]
rs34326553	0.93[EUR][1000 genomes]
rs34343820	0.81[EUR][1000 genomes]
rs34477108	0.85[AMR][1000 genomes]
rs34504524	1.00[AMR][1000 genomes]
rs34509487	0.85[AMR][1000 genomes]
rs34566463	0.88[EUR][1000 genomes]
rs34580506	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34784192	0.86[EUR][1000 genomes]
rs34889065	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35060561	0.88[EUR][1000 genomes]
rs35102816	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35108630	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35185152	0.86[EUR][1000 genomes]
rs35283189	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35673421	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3923475	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5030795	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55921200	0.81[EUR][1000 genomes]
rs56004653	0.88[AMR][1000 genomes]
rs56306491	0.86[EUR][1000 genomes]
rs56318350	0.83[AMR][1000 genomes]
rs61729488	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66991555	0.88[EUR][1000 genomes]
rs67060340	0.82[AMR][1000 genomes]
rs67286839	0.86[EUR][1000 genomes]
rs67332931	0.85[AMR][1000 genomes]
rs67831908	0.81[EUR][1000 genomes]
rs71324924	0.85[AMR][1000 genomes]
rs71324929	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71324939	0.86[EUR][1000 genomes]
rs73082362	0.88[AMR][1000 genomes]
rs73084135	0.91[EUR][1000 genomes]
rs9311439	0.81[EUR][1000 genomes]
rs9814987	0.87[EUR][1000 genomes]
rs9826525	0.86[EUR][1000 genomes]
rs9828310	0.86[EUR][1000 genomes]
rs9835439	0.83[EUR][1000 genomes]
rs9837237	0.88[EUR][1000 genomes]
rs9837625	0.88[EUR][1000 genomes]
rs9847839	0.86[EUR][1000 genomes]
rs9850917	0.86[EUR][1000 genomes]
rs9855123	0.88[EUR][1000 genomes]
rs9862483	0.88[EUR][1000 genomes]
rs9880088	0.91[EUR][1000 genomes]
rs9880309	0.81[EUR][1000 genomes]
rs9990153	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11718982	WDR6	cis	Adipose Subcutaneous	GTEx
rs11718982	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11718982	WDR6	cis	Artery Tibial	GTEx
rs11718982	WDR6	cis	Whole Blood	GTEx
rs11718982	WDR6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49129600-49132600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:49129800-49132600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr3:49129800-49132600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr3:49129800-49132600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:49129800-49132600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:49129800-49132600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr3:49129800-49132600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr3:49130000-49132600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr3:49130200-49132800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:49130200-49132800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:49130400-49132600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr3:49130400-49132600	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr3:49130400-49132600	Active TSS	Fetal Lung	lung
14	chr3:49130400-49132800	Active TSS	Rectal Smooth Muscle	rectum
15	chr3:49131000-49132600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:49131800-49132600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:49131800-49132600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr3:49131800-49132600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:49131800-49132600	Flanking Active TSS	Dnd41	blood
20	chr3:49132000-49132600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr3:49132000-49132600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr3:49132000-49132600	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr3:49132000-49132600	Enhancers	Fetal Heart	heart
24	chr3:49132000-49132600	Flanking Active TSS	Fetal Intestine Small	intestine
25	chr3:49132000-49132600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr3:49132000-49132600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr3:49132000-49132600	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr3:49132000-49132600	Enhancers	Spleen	Spleen
29	chr3:49132000-49132600	Flanking Active TSS	Hela-S3	cervix
30	chr3:49132000-49132600	Flanking Active TSS	K562	blood
31	chr3:49132000-49133600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:49132200-49132600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:49132200-49132600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:49132200-49132600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:49132200-49132600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:49132200-49132600	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr3:49132200-49132600	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr3:49132200-49132600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr3:49132200-49132800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:49132200-49133400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:49132400-49132600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:49132400-49132600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:49132400-49132600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr3:49132400-49132600	Enhancers	Primary B cells from cord blood	blood
45	chr3:49132400-49132600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr3:49132400-49132600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:49132400-49132600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr3:49132400-49132600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:49132400-49132600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr3:49132400-49132600	Enhancers	Cortex derived primary cultured neurospheres	brain

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