Variant report

Variant	rs6969779
Chromosome Location	chr7:140399747-140399748
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:140399083-140399840	K562	blood:	n/a	n/a
2	MAFF	chr7:140399730-140399930	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:140370275..140375389-chr7:140393210..140401279,16	MCF-7	breast:
2	chr7:140394719..140399884-chr7:140712014..140716961,9	K562	blood:
3	chr7:140395386..140400852-chr7:140710628..140716984,11	MCF-7	breast:

Variant related genes	Relation type
NDUFB2-AS1	TF binding region
NDUFB2	TF binding region
ENSG00000146966	Chromatin interaction
ENSG00000133597	Chromatin interaction
ENSG00000090263	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]
rs4727053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
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
rs6969779	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140397600-140407400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:140397800-140403200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:140397800-140405800	Weak transcription	Aorta	Aorta
4	chr7:140397800-140406800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:140398000-140399800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:140398000-140399800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr7:140398000-140399800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr7:140398000-140399800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr7:140398000-140402400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:140398000-140402800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:140398000-140404000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:140398000-140404000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:140398000-140404000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:140398000-140406000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:140398000-140406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:140398000-140408800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:140398000-140419400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr7:140398000-140466600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:140398200-140399800	Enhancers	HepG2	liver
20	chr7:140398200-140401200	Weak transcription	Liver	Liver
21	chr7:140398200-140402400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:140398200-140402400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr7:140398200-140402400	Weak transcription	A549	lung
24	chr7:140398200-140402600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:140398200-140402600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:140398200-140402600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr7:140398200-140402600	Weak transcription	Thymus	Thymus
28	chr7:140398200-140402600	Weak transcription	HSMMtube	muscle
29	chr7:140398200-140402600	Weak transcription	HUVEC	blood vessel
30	chr7:140398200-140403400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr7:140398200-140403800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:140398200-140403800	Weak transcription	Osteobl	bone
33	chr7:140398200-140404000	Weak transcription	Lung	lung
34	chr7:140398200-140406000	Weak transcription	Fetal Lung	lung
35	chr7:140398200-140406000	Weak transcription	HSMM	muscle
36	chr7:140398200-140473800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr7:140398200-140492600	Weak transcription	Colonic Mucosa	Colon
38	chr7:140398400-140402200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:140398400-140402400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:140398400-140402600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr7:140398400-140402600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr7:140398400-140402600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:140398400-140402600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr7:140398400-140402800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:140398400-140402800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:140398400-140403800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr7:140398400-140404000	Weak transcription	Primary B cells from cord blood	blood
48	chr7:140398400-140404000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr7:140398400-140404000	Weak transcription	Adipose Nuclei	Adipose
50	chr7:140398400-140404000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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