Variant report

Variant	rs4855877
Chromosome Location	chr3:49448527-49448528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:49448142-49450226	GM12878	blood:	n/a	n/a
2	WRNIP1	chr3:49448480-49448988	GM12878	blood:	n/a	n/a
3	MAX	chr3:49448496-49450106	Hela-S3	cervix:	n/a	chr3:49448867-49448876 chr3:49448924-49448934 chr3:49449585-49449594
4	CUX1	chr3:49448301-49448829	K562	blood:	n/a	chr3:49448775-49448784 chr3:49448496-49448505
5	POLR2A	chr3:49448355-49448755	HUVEC	blood vessel:	n/a	n/a
6	HCFC1	chr3:49448164-49450849	Hela-S3	cervix:	n/a	n/a
7	CUX1	chr3:49448127-49448665	GM12878	blood:	n/a	chr3:49448496-49448505
8	POLR2A	chr3:49448417-49448608	MCF-7	breast:	n/a	n/a
9	POLR2A	chr3:49448292-49450804	IMR90	lung:	n/a	n/a
10	POLR2A	chr3:49448395-49450585	PBDE	blood:	n/a	n/a
11	CHD1	chr3:49446752-49450840	IMR90	lung:	n/a	n/a
12	POLR2A	chr3:49448379-49448669	Hela-S3	cervix:	n/a	n/a
13	CHD1	chr3:49448365-49449347	H1-hESC	embryonic stem cell:	n/a	n/a
14	RELA	chr3:49448514-49450624	GM10847	blood:	n/a	n/a
15	TAF1	chr3:49448522-49449068	Hela-S3	cervix:	n/a	n/a
16	TCF12	chr3:49448484-49449103	A549	lung:	n/a	n/a
17	MYC	chr3:49448503-49449987	MCF10A-Er-Src	breast:	n/a	chr3:49448867-49448876 chr3:49448924-49448934 chr3:49449585-49449594
18	GATA3	chr3:49448320-49448627	SH-SY5Y	brain:	n/a	n/a
19	GATA1	chr3:49448378-49450207	PBDE	blood:	n/a	n/a
20	SIN3A	chr3:49448407-49450296	H1-hESC	embryonic stem cell:	n/a	n/a
21	MXI1	chr3:49447410-49450981	SK-N-SH	brain:	n/a	n/a
22	MXI1	chr3:49447853-49450922	IMR90	lung:	n/a	n/a
23	STAT3	chr3:49447347-49448591	GM12878	blood:	n/a	n/a
24	TBP	chr3:49448324-49448547	GM12878	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49447135..49449560-chr3:49709671..49711727,2	K562	blood:
2	chr3:49387350..49389031-chr3:49446931..49448922,3	K562	blood:
3	chr3:49375112..49379681-chr3:49446166..49452291,17	K562	blood:
4	chr3:49203572..49205247-chr3:49448132..49451113,3	MCF-7	breast:
5	chr3:49064721..49066912-chr3:49446904..49449709,2	K562	blood:
6	chr3:49394592..49396828-chr3:49447365..49450223,2	K562	blood:
7	chr3:49130018..49132497-chr3:49447157..49449829,4	K562	blood:
8	chr3:49447402..49451449-chr3:49505916..49509646,7	K562	blood:
9	chr3:49375789..49379333-chr3:49446166..49450939,13	K562	blood:
10	chr3:49424540..49427374-chr3:49447605..49449353,2	MCF-7	breast:
11	chr3:49448236..49450769-chr3:49505936..49509558,3	MCF-7	breast:
12	chr3:49377084..49379212-chr3:49447955..49450362,2	MCF-7	breast:
13	chr3:49438129..49440566-chr3:49446328..49448559,2	K562	blood:
14	chr3:49054710..49056578-chr3:49447542..49450495,2	K562	blood:
15	chr3:49447402..49452044-chr3:49506038..49509646,9	K562	blood:
16	chr3:49129916..49132990-chr3:49447157..49451022,6	K562	blood:
17	chr3:49447469..49451415-chr3:49463621..49468909,12	K562	blood:

No data

Variant related genes	Relation type
TCTA	TF binding region
ENSG00000173402	Chromatin interaction
ENSG00000233276	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000145029	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000198218	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1050088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10640	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10865955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130192	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130193	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130194	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11130196	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130202	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11706370	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11711485	1.00[JPT][hapmap]
rs11715915	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11716974	0.86[ASN][1000 genomes]
rs11720264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11922013	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12488065	0.83[EUR][1000 genomes]
rs12489092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13078949	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs13079643	0.86[ASN][1000 genomes]
rs13096760	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1464566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs1568662	0.84[EUR][1000 genomes]
rs17080528	1.00[JPT][hapmap]
rs17595772	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17650792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1800668	1.00[JPT][hapmap]
rs1801143	1.00[JPT][hapmap]
rs1987628	1.00[JPT][hapmap]
rs2117939	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2312461	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2878298	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34937635	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35115732	0.86[ASN][1000 genomes]
rs35701831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3811697	1.00[JPT][hapmap]
rs3811699	1.00[JPT][hapmap]
rs3870337	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3870338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3877784	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3924462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3924463	0.83[EUR][1000 genomes]
rs4241406	0.81[EUR][1000 genomes]
rs4241408	0.82[EUR][1000 genomes]
rs4459909	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563439	0.89[EUR][1000 genomes]
rs4625	1.00[JPT][hapmap]
rs4855836	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4855842	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4855843	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855855	0.81[EUR][1000 genomes]
rs4855859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855861	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855866	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4855873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955412	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4955438	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55957735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59152804	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62259939	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62259942	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62261185	0.82[EUR][1000 genomes]
rs6446272	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6446274	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6446277	0.86[ASN][1000 genomes]
rs6766131	1.00[JPT][hapmap]
rs6773518	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6779524	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6782577	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[YRI][hapmap]
rs6784820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792911	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6797765	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6997	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7371895	0.83[EUR][1000 genomes]
rs7373849	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7621003	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7622302	1.00[JPT][hapmap]
rs7631908	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7633271	1.00[JPT][hapmap]
rs7637665	0.81[EUR][1000 genomes]
rs7637999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7643586	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7643845	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7645445	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7646366	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs885592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9814873	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9827021	1.00[JPT][hapmap]
rs9837027	1.00[JPT][hapmap]
rs9841110	1.00[JPT][hapmap]
rs9853683	1.00[JPT][hapmap]
rs9858280	1.00[JPT][hapmap]
rs9859556	0.90[ASN][1000 genomes]
rs9871380	0.94[ASN][1000 genomes]
rs9875617	1.00[JPT][hapmap]
rs9878943	0.94[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4855877	WDR6	cis	Muscle Skeletal	GTEx
rs4855877	WDR6	cis	Whole Blood	GTEx
rs4855877	WDR6	cis	lung	GTEx
rs4855877	AMT	cis	Thyroid	GTEx
rs4855877	WDR6	cis	Nerve Tibial	GTEx
rs4855877	WDR6	cis	Artery Tibial	GTEx
rs4855877	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs4855877	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4855877	WDR6	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49444600-49448600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:49446000-49450200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:49446800-49448600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:49446800-49448800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr3:49446800-49450400	Active TSS	NHLF	lung
6	chr3:49447000-49448600	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr3:49447000-49448600	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr3:49447000-49450200	Active TSS	HSMMtube	muscle
9	chr3:49447000-49450400	Active TSS	Ovary	ovary
10	chr3:49447000-49450600	Active TSS	Aorta	Aorta
11	chr3:49447200-49448600	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr3:49447200-49448600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr3:49447200-49448600	Flanking Active TSS	Brain Angular Gyrus	brain
14	chr3:49447200-49448600	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr3:49447200-49448600	Flanking Active TSS	Fetal Heart	heart
16	chr3:49447200-49448800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr3:49447200-49449400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:49447200-49449800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:49447200-49450400	Active TSS	Left Ventricle	heart
20	chr3:49447400-49448600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:49447400-49448800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:49447400-49449800	Active TSS	Fetal Muscle Trunk	muscle
23	chr3:49447400-49450200	Active TSS	Lung	lung
24	chr3:49447400-49450400	Active TSS	H9 Cell Line	embryonic stem cell
25	chr3:49447600-49448800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr3:49447600-49448800	Weak transcription	Spleen	Spleen
27	chr3:49447600-49449000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr3:49447600-49450200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:49447600-49450400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr3:49447600-49450400	Active TSS	Right Ventricle	heart
31	chr3:49447600-49450400	Active TSS	A549	lung
32	chr3:49447600-49450600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:49447800-49448600	Transcr. at gene 5' and 3'	HSMM	muscle
34	chr3:49447800-49449000	Active TSS	Stomach Mucosa	stomach
35	chr3:49447800-49449200	Active TSS	Right Atrium	heart
36	chr3:49447800-49449800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:49447800-49450000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:49447800-49450000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:49447800-49450000	Active TSS	Fetal Thymus	thymus
40	chr3:49447800-49450200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:49447800-49450200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:49447800-49450200	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr3:49447800-49450200	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr3:49447800-49450400	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr3:49447800-49450400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:49447800-49450400	Active TSS	Fetal Kidney	kidney
47	chr3:49447800-49450400	Active TSS	Placenta Amnion	Placenta Amnion
48	chr3:49447800-49450400	Active TSS	GM12878-XiMat	blood
49	chr3:49447800-49450400	Active TSS	NHDF-Ad	bronchial
50	chr3:49448000-49448800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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