Variant report

Variant	rs3923475
Chromosome Location	chr3:49055788-49055789
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:337)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:337 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49055271-49056245	GM10847	blood:	n/a	n/a
2	POLR2A	chr3:49054926-49056367	GM18951	blood:	n/a	n/a
3	ELF1	chr3:49055746-49056375	K562	blood:	n/a	chr3:49056017-49056030
4	YY1	chr3:49055554-49056190	SK-N-SH_RA	brain:	n/a	n/a
5	CREB1	chr3:49055337-49056284	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49052944-49056404	MCF10A-Er-Src	breast:	n/a	n/a
7	ZC3H11A	chr3:49055729-49055972	K562	blood:	n/a	n/a
8	YY1	chr3:49055258-49056270	GM12892	blood:	n/a	n/a
9	PML	chr3:49054928-49056240	MCF-7	breast:	n/a	n/a
10	POLR2A	chr3:49055777-49056194	A549	lung:	n/a	n/a
11	CREB1	chr3:49054822-49056333	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:49055048-49056296	K562	blood:	n/a	n/a
13	SIN3AK20	chr3:49055716-49056028	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr3:49054985-49056467	K562	blood:	n/a	n/a
15	POLR2A	chr3:49054864-49056401	MCF-7	breast:	n/a	n/a
16	ZMIZ1	chr3:49055364-49056044	K562	blood:	n/a	n/a
17	MXI1	chr3:49055106-49056504	K562	blood:	n/a	n/a
18	TBP	chr3:49055781-49056365	K562	blood:	n/a	n/a
19	POLR2A	chr3:49055738-49056439	GM12892	blood:	n/a	n/a
20	CREB1	chr3:49055596-49056136	ECC-1	luminal epithelium:	n/a	n/a
21	GATA3	chr3:49055107-49056395	A549	lung:	n/a	n/a
22	SIN3AK20	chr3:49055719-49056150	HepG2	liver:	n/a	n/a
23	CREB1	chr3:49055193-49056312	K562	blood:	n/a	n/a
24	HEY1	chr3:49055643-49056148	K562	blood:	n/a	n/a
25	UBTF	chr3:49055004-49056493	K562	blood:	n/a	n/a
26	POLR2A	chr3:49054895-49056408	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr3:49050113-49067296	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:49053148-49056378	GM12878	blood:	n/a	n/a
29	MAX	chr3:49055022-49056192	MCF-7	breast:	n/a	n/a
30	CHD2	chr3:49055738-49055923	K562	blood:	n/a	n/a
31	YY1	chr3:49055550-49056262	GM12878	blood:	n/a	n/a
32	GABPA	chr3:49055379-49056342	K562	blood:	n/a	chr3:49056014-49056021
33	TAF1	chr3:49055661-49056121	K562	blood:	n/a	n/a
34	POLR2A	chr3:49054945-49056474	HCT-116	colon:	n/a	n/a
35	POLR2A	chr3:49055617-49056619	GM12892	blood:	n/a	n/a
36	GABPA	chr3:49055675-49056174	GM12878	blood:	n/a	chr3:49056014-49056021
37	JUND	chr3:49055536-49056249	A549	lung:	n/a	n/a
38	SMC3	chr3:49055643-49055975	Hela-S3	cervix:	n/a	n/a
39	SP1	chr3:49055600-49056036	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:49055125-49056438	GM18505	blood:	n/a	n/a
41	POLR2A	chr3:49052980-49056417	HL-60	blood:	n/a	n/a
42	POLR2A	chr3:49055774-49056362	K562	blood:	n/a	n/a
43	ZBTB7A	chr3:49055751-49056329	K562	blood:	n/a	chr3:49056085-49056096 chr3:49056157-49056164 chr3:49056279-49056290
44	FOSL2	chr3:49055660-49056244	HepG2	liver:	n/a	n/a
45	POLR2A	chr3:49051503-49056616	SK-N-SH	brain:	n/a	n/a
46	HMGN3	chr3:49055115-49056246	K562	blood:	n/a	n/a
47	YY1	chr3:49055137-49056222	HepG2	liver:	n/a	n/a
48	ATF2	chr3:49055331-49056490	GM12878	blood:	n/a	n/a
49	MAX	chr3:49055452-49056040	A549	lung:	n/a	n/a
50	NR2F2	chr3:49055443-49056154	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:20409291..20409979-chr3:49055367..49056087,2	HCT-116	colon:
2	chr20:62151892..62152418-chr3:49055180..49055966,2	Hela-S3	cervix:
3	chr3:49054288..49061452-chr3:49128946..49133927,24	K562	blood:
4	chr3:49055445..49060745-chr3:49128874..49135153,17	MCF-7	breast:
5	chr14:105265057..105267677-chr3:49054198..49056753,2	MCF-7	breast:
6	chr3:49052218..49068794-chr3:49126865..49133927,44	K562	blood:
7	chr3:49055428..49056396-chr7:32931996..32932598,2	Hela-S3	cervix:
8	chr3:48720679..48723641-chr3:49054826..49057455,2	K562	blood:
9	chr3:49055528..49056300-chr4:103422455..103423039,2	HCT-116	colon:
10	chr19:2236080..2236926-chr3:49055246..49055917,2	HCT-116	colon:
11	chr3:49054710..49056578-chr3:49447542..49450495,2	K562	blood:

No data

Variant related genes	Relation type
DALRD3	TF binding region
NDUFAF3	TF binding region
ENSG00000213672	Chromatin interaction
ENSG00000185238	Chromatin interaction
ENSG00000104897	Chromatin interaction
ENSG00000125534	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000170852	Chromatin interaction
ENSG00000260651	Chromatin interaction
ENSG00000104886	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000109320	Chromatin interaction
ENSG00000179627	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10154895	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11552724	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706189	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11708022	0.85[AMR][1000 genomes]
rs11709092	0.81[AMR][1000 genomes]
rs11709246	0.85[AMR][1000 genomes]
rs11710247	0.82[EUR][1000 genomes]
rs11712006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713297	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11713694	0.85[AMR][1000 genomes]
rs11715689	0.89[AMR][1000 genomes]
rs11715713	0.89[AMR][1000 genomes]
rs11715835	0.85[AMR][1000 genomes]
rs11716614	0.88[AMR][1000 genomes]
rs11717978	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11718982	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11719220	0.82[EUR][1000 genomes]
rs11719457	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12493001	0.81[ASN][1000 genomes]
rs12636030	0.81[ASN][1000 genomes]
rs12637037	0.92[ASN][1000 genomes]
rs13064784	0.82[ASN][1000 genomes]
rs13064911	0.82[ASN][1000 genomes]
rs13072554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073997	0.85[AMR][1000 genomes]
rs13074318	0.85[AMR][1000 genomes]
rs13080725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084000	0.85[AMR][1000 genomes]
rs13086240	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13087930	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13090839	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13094900	0.82[AMR][1000 genomes]
rs13096406	0.84[EUR][1000 genomes]
rs13316620	0.84[ASN][1000 genomes]
rs3212	0.82[ASN][1000 genomes]
rs34326553	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34477108	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34504524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34509487	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34566463	0.82[EUR][1000 genomes]
rs34580506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34889065	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35060561	0.82[EUR][1000 genomes]
rs35102816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35108630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35283189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35673421	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4072859	0.89[ASN][1000 genomes]
rs4279134	0.82[ASN][1000 genomes]
rs4364202	0.80[ASN][1000 genomes]
rs4513485	0.82[ASN][1000 genomes]
rs4521268	0.82[ASN][1000 genomes]
rs4974080	0.85[ASN][1000 genomes]
rs5030795	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56004653	0.88[AMR][1000 genomes]
rs56318350	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61729488	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62262517	0.80[ASN][1000 genomes]
rs6414613	0.85[ASN][1000 genomes]
rs6446196	0.84[ASN][1000 genomes]
rs6446198	0.82[ASN][1000 genomes]
rs6446205	0.85[ASN][1000 genomes]
rs66991555	0.84[EUR][1000 genomes]
rs67060340	0.82[AMR][1000 genomes]
rs67332931	0.85[AMR][1000 genomes]
rs6779394	0.87[ASN][1000 genomes]
rs6781790	0.85[ASN][1000 genomes]
rs6784111	0.81[ASN][1000 genomes]
rs6789285	0.89[ASN][1000 genomes]
rs6795025	1.00[ASN][1000 genomes]
rs71324924	0.85[AMR][1000 genomes]
rs71324929	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73082362	0.88[AMR][1000 genomes]
rs7373790	0.92[ASN][1000 genomes]
rs7430198	0.82[ASN][1000 genomes]
rs7432989	0.90[ASN][1000 genomes]
rs7615235	0.90[ASN][1000 genomes]
rs7626445	0.82[ASN][1000 genomes]
rs7639332	0.82[ASN][1000 genomes]
rs8926	0.90[ASN][1000 genomes]
rs9814987	0.83[EUR][1000 genomes]
rs9835439	0.81[ASN][1000 genomes]
rs9837237	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837625	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9840050	0.82[ASN][1000 genomes]
rs9846123	0.95[ASN][1000 genomes]
rs9855123	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9862483	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9880088	0.86[EUR][1000 genomes];0.81[ASN][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	esv3323398	chr3:49053998-49056796	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	esv3339864	chr3:49054573-49057121	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3923475	WDR6	cis	Artery Tibial	GTEx
rs3923475	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs3923475	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs3923475	WDR6	cis	Adipose Subcutaneous	GTEx
rs3923475	WDR6	cis	Esophagus Mucosa	GTEx
rs3923475	WDR6	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49053400-49056000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:49054400-49057600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:49054600-49056200	Enhancers	Fetal Brain Male	brain
4	chr3:49054600-49056400	Active TSS	NHDF-Ad	bronchial
5	chr3:49054600-49056600	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr3:49054600-49056800	Flanking Active TSS	Dnd41	blood
7	chr3:49054600-49057600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:49054800-49055800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr3:49054800-49055800	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr3:49054800-49055800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr3:49054800-49056600	Active TSS	Fetal Kidney	kidney
12	chr3:49054800-49056600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr3:49054800-49057400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr3:49054800-49060400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr3:49055000-49055800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:49055000-49055800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr3:49055000-49055800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:49055000-49056400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr3:49055000-49056400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:49055000-49056600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:49055000-49056600	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr3:49055000-49056800	Flanking Active TSS	Liver	Liver
23	chr3:49055000-49057400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr3:49055200-49056000	Transcr. at gene 5' and 3'	Right Atrium	heart
25	chr3:49055200-49056200	Active TSS	Fetal Brain Female	brain
26	chr3:49055200-49056400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:49055200-49056400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:49055200-49056400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:49055200-49056400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:49055200-49056400	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr3:49055200-49056400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:49055200-49056400	Active TSS	Colon Smooth Muscle	Colon
33	chr3:49055200-49056400	Active TSS	Fetal Lung	lung
34	chr3:49055200-49056400	Active TSS	Small Intestine	intestine
35	chr3:49055200-49056600	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr3:49055200-49056600	Active TSS	Psoas Muscle	Psoas
37	chr3:49055200-49056600	Active TSS	Sigmoid Colon	Sigmoid Colon
38	chr3:49055200-49056600	Active TSS	A549	lung
39	chr3:49055200-49056600	Active TSS	NHLF	lung
40	chr3:49055200-49057200	Active TSS	GM12878-XiMat	blood
41	chr3:49055200-49057400	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr3:49055200-49057400	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr3:49055200-49060400	Active TSS	K562	blood
44	chr3:49055200-49060600	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr3:49055400-49055800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:49055400-49056000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr3:49055400-49056000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:49055400-49056200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:49055400-49056200	Active TSS	Primary B cells from peripheral blood	blood
50	chr3:49055400-49056200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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