Variant report

Variant	rs6767878
Chromosome Location	chr3:49710345-49710346
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49709792-49716426	HepG2	liver:	n/a	n/a
2	ZNF384	chr3:49710110-49710918	K562	blood:	n/a	chr3:49710793-49710801

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49575867..49578786-chr3:49708422..49711347,4	K562	blood:
2	chr3:49570124..49571961-chr3:49709583..49711115,2	MCF-7	breast:
3	chr3:49709764..49714141-chr3:49724462..49728582,8	MCF-7	breast:
4	chr3:49064195..49067148-chr3:49710210..49713126,3	MCF-7	breast:
5	chr3:49709585..49712525-chr3:49736619..49738353,2	K562	blood:
6	chr3:49590547..49592695-chr3:49709214..49711684,3	MCF-7	breast:
7	chr3:49577156..49579797-chr3:49709101..49710779,3	K562	blood:
8	chr3:49590294..49593133-chr3:49709342..49710868,2	K562	blood:
9	chr3:49710197..49713072-chr3:49759630..49762760,3	MCF-7	breast:
10	chr3:49603620..49605380-chr3:49707989..49710873,2	MCF-7	breast:
11	chr3:49506494..49510419-chr3:49709515..49713189,4	MCF-7	breast:
12	chr3:49447135..49449560-chr3:49709671..49711727,2	K562	blood:
13	chr3:49687205..49689854-chr3:49709727..49711348,2	MCF-7	breast:
14	chr3:49505441..49508480-chr3:49710122..49713377,5	MCF-7	breast:
15	chr3:49043665..49045561-chr3:49710277..49712167,2	K562	blood:
16	chr3:49449662..49452069-chr3:49709335..49712259,2	K562	blood:
17	chr3:49709088..49712884-chr3:49714614..49717582,5	MCF-7	breast:
18	chr3:49708866..49715375-chr3:49724746..49730407,6	K562	blood:

No data

Variant related genes	Relation type
APEH	TF binding region
ENSG00000145022	Chromatin interaction
ENSG00000226913	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000164061	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000173540	Chromatin interaction
ENSG00000173531	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000178035	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1060962	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11130212	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11919311	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12497288	0.80[EUR][1000 genomes]
rs1352890	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1873626	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2005557	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2131104	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2131109	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2329020	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2960548	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35007338	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35404120	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4855847	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4855852	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4855881	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4855883	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4855884	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6765869	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6767878	WDR6	cis	Nerve Tibial	GTEx
rs6767878	WDR6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
2	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
3	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:49700000-49710600	Weak transcription	Fetal Brain Male	brain
6	chr3:49702400-49710600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49703600-49710600	Weak transcription	Left Ventricle	heart
8	chr3:49703600-49710600	Weak transcription	Right Ventricle	heart
9	chr3:49703600-49710600	Weak transcription	Spleen	Spleen
10	chr3:49703800-49710600	Enhancers	Liver	Liver
11	chr3:49703800-49710600	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:49704200-49710600	Weak transcription	Gastric	stomach
13	chr3:49704400-49710600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:49704600-49710600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:49704600-49710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:49704800-49710600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:49705000-49710600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:49705600-49710600	Weak transcription	Brain Anterior Caudate	brain
19	chr3:49705600-49710600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:49705600-49710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:49706000-49710600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:49706200-49710600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:49706200-49710600	Weak transcription	Brain Angular Gyrus	brain
24	chr3:49706200-49710600	Weak transcription	Fetal Intestine Large	intestine
25	chr3:49706200-49710600	Weak transcription	Fetal Intestine Small	intestine
26	chr3:49706800-49710600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:49706800-49710600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:49706800-49710600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:49706800-49710600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:49706800-49710600	Weak transcription	Stomach Mucosa	stomach
31	chr3:49707000-49710600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:49707000-49710600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:49707000-49710600	Weak transcription	Adipose Nuclei	Adipose
34	chr3:49707000-49710600	Weak transcription	Esophagus	oesophagus
35	chr3:49707000-49710600	Weak transcription	Fetal Muscle Leg	muscle
36	chr3:49707000-49710600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:49707000-49710600	Weak transcription	HSMM	muscle
38	chr3:49707000-49710600	Weak transcription	NH-A	brain
39	chr3:49707000-49710600	Weak transcription	NHEK	skin
40	chr3:49707000-49710600	Weak transcription	Osteobl	bone
41	chr3:49707200-49710600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:49707200-49710600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:49707200-49710600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:49707200-49710600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:49707200-49710600	Weak transcription	HSMMtube	muscle
46	chr3:49707400-49710600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:49708200-49710600	Weak transcription	Brain Germinal Matrix	brain
48	chr3:49708400-49710600	Weak transcription	Fetal Brain Female	brain
49	chr3:49709000-49710600	Enhancers	Placenta	Placenta
50	chr3:49709000-49710600	Enhancers	K562	blood

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