Variant report

Variant	rs4727053
Chromosome Location	chr7:140398149-140398150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:140395412-140398733	K562	blood:	n/a	n/a
2	POLR2A	chr7:140396312-140398555	A549	lung:	n/a	n/a
3	IRF1	chr7:140398121-140398202	K562	blood:	n/a	n/a
4	POLR2A	chr7:140395870-140398317	K562	blood:	n/a	n/a
5	SREBP1	chr7:140395610-140398289	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:140395805..140398704-chr7:140623265..140626329,4	K562	blood:
2	chr7:140175625..140180151-chr7:140394567..140398370,5	MCF-7	breast:
3	chr7:140370275..140375389-chr7:140393210..140401279,16	MCF-7	breast:
4	chr7:140394719..140399884-chr7:140712014..140716961,9	K562	blood:
5	chr7:140395267..140398426-chr7:140622802..140626309,6	K562	blood:
6	chr7:140394556..140398514-chr7:140712637..140716961,7	K562	blood:
7	chr7:140394845..140398499-chr7:140712009..140715919,6	MCF-7	breast:
8	chr7:140176812..140180644-chr7:140393947..140398398,4	K562	blood:
9	chr7:140371560..140374067-chr7:140396511..140398663,2	K562	blood:
10	chr7:140395386..140400852-chr7:140710628..140716984,11	MCF-7	breast:
11	chr7:140370608..140383131-chr7:140387718..140398587,28	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFB2	TF binding region
NDUFB2-AS1	TF binding region
ENSG00000157764	Chromatin interaction
ENSG00000133597	Chromatin interaction
ENSG00000090263	Chromatin interaction
ENSG00000133606	Chromatin interaction
ENSG00000146966	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10241711	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10242534	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10260676	0.81[ASN][1000 genomes]
rs1046515	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12375245	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267609	0.84[EUR][1000 genomes]
rs1267611	0.84[EUR][1000 genomes]
rs1267613	0.87[EUR][1000 genomes]
rs1267614	0.87[EUR][1000 genomes]
rs1267617	0.87[EUR][1000 genomes]
rs1267633	0.80[EUR][1000 genomes]
rs1267636	0.85[EUR][1000 genomes]
rs1267638	0.87[EUR][1000 genomes]
rs1267639	0.84[EUR][1000 genomes]
rs1267640	0.87[EUR][1000 genomes]
rs1267642	0.87[EUR][1000 genomes]
rs1267644	0.87[EUR][1000 genomes]
rs1267649	0.87[EUR][1000 genomes]
rs1270193	0.87[EUR][1000 genomes]
rs1639675	0.87[EUR][1000 genomes]
rs1639678	0.87[EUR][1000 genomes]
rs1639679	0.84[EUR][1000 genomes]
rs17161666	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161668	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17161737	0.80[EUR][1000 genomes]
rs1733827	0.87[EUR][1000 genomes]
rs1733832	0.87[EUR][1000 genomes]
rs1812162	0.98[EUR][1000 genomes]
rs2245716	0.87[EUR][1000 genomes]
rs2364396	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2364397	0.81[ASN][1000 genomes]
rs2364398	0.95[EUR][1000 genomes]
rs2535951	0.85[EUR][1000 genomes]
rs28517771	0.85[ASN][1000 genomes]
rs28577882	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2907950	0.85[ASN][1000 genomes]
rs2930315	0.83[ASN][1000 genomes]
rs2930318	0.83[ASN][1000 genomes]
rs2930319	0.83[ASN][1000 genomes]
rs2968549	0.86[ASN][1000 genomes]
rs2968550	0.86[ASN][1000 genomes]
rs2968551	0.85[ASN][1000 genomes]
rs2968553	0.83[ASN][1000 genomes]
rs2968555	0.81[ASN][1000 genomes]
rs4725799	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4727021	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4727036	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4727040	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4727041	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464036	0.87[EUR][1000 genomes]
rs6464984	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6949396	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6962426	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6969779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977834	0.86[ASN][1000 genomes]
rs73489531	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73489562	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73491672	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73491871	0.87[EUR][1000 genomes]
rs73505645	0.85[ASN][1000 genomes]
rs73505647	0.87[ASN][1000 genomes]
rs7792746	0.87[ASN][1000 genomes]
rs7803697	0.86[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	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv3351231	chr7:140390303-140588539	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv831158	chr7:140392222-140602315	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4727053	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140396000-140398200	Active TSS	HSMMtube	muscle
2	chr7:140396200-140398200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:140396400-140398200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:140396600-140398200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
5	chr7:140397000-140398400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr7:140397200-140398200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:140397200-140398200	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr7:140397200-140398200	Flanking Active TSS	Fetal Thymus	thymus
9	chr7:140397200-140398200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr7:140397200-140398200	Flanking Active TSS	Osteobl	bone
11	chr7:140397200-140398400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr7:140397400-140398200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr7:140397400-140398200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:140397400-140398200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:140397400-140398200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr7:140397400-140398200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:140397400-140398200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:140397400-140398200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:140397400-140398200	Flanking Active TSS	Brain Angular Gyrus	brain
20	chr7:140397400-140398200	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr7:140397400-140398200	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr7:140397400-140398200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr7:140397400-140398200	Flanking Active TSS	Brain Substantia Nigra	brain
24	chr7:140397400-140398200	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr7:140397400-140398200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr7:140397400-140398200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr7:140397400-140398200	Flanking Active TSS	HepG2	liver
28	chr7:140397400-140398200	Flanking Active TSS	K562	blood
29	chr7:140397400-140398200	Flanking Active TSS	NH-A	brain
30	chr7:140397400-140398400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:140397400-140398400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:140397400-140398400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:140397400-140398400	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr7:140397400-140398400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:140397400-140398400	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr7:140397400-140398400	Flanking Active TSS	Fetal Brain Female	brain
37	chr7:140397400-140398400	Flanking Active TSS	NHEK	skin
38	chr7:140397400-140398600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:140397600-140398200	Flanking Active TSS	Colonic Mucosa	Colon
40	chr7:140397600-140398200	Flanking Active TSS	Psoas Muscle	Psoas
41	chr7:140397600-140398200	Flanking Active TSS	Hela-S3	cervix
42	chr7:140397600-140398200	Flanking Active TSS	NHDF-Ad	bronchial
43	chr7:140397600-140398400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:140397600-140398400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr7:140397600-140398400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:140397600-140398400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr7:140397600-140398400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr7:140397600-140398400	Flanking Active TSS	Right Ventricle	heart
49	chr7:140397600-140398400	Enhancers	Stomach Mucosa	stomach
50	chr7:140397600-140398400	Flanking Active TSS	Stomach Smooth Muscle	stomach

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