Variant report

Variant	rs62485366
Chromosome Location	chr7:140589660-140589661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140559633..140561782-chr7:140587885..140590240,2	MCF-7	breast:
2	chr7:140583613..140585330-chr7:140588993..140590809,2	K562	blood:
3	chr7:140589437..140591945-chr7:140623059..140625802,2	K562	blood:
4	chr7:140589226..140590844-chr7:140624439..140626444,2	MCF-7	breast:
5	chr7:140588302..140590134-chr7:140608160..140610912,2	K562	blood:
6	chr7:140588144..140589724-chr7:140618968..140621680,2	K562	blood:
7	chr7:140585371..140588493-chr7:140589347..140593837,4	K562	blood:

Variant related genes	Relation type
ENSG00000271932	Chromatin interaction
ENSG00000157764	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1009772	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10281975	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10488098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11983228	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13438418	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1476868	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17622717	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17623204	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17695341	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17695623	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17695707	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17695935	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17695995	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968140	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2079827	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs246739	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2930322	0.84[EUR][1000 genomes]
rs41282721	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55720380	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55875248	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56055746	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56115934	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56347011	0.95[EUR][1000 genomes]
rs56940988	0.80[ASN][1000 genomes]
rs57143942	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57620608	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57675404	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57725920	0.83[EUR][1000 genomes]
rs57846481	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58901822	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59183598	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59232128	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59477283	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59816436	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60081231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60187684	0.82[ASN][1000 genomes]
rs60251368	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61421775	0.80[ASN][1000 genomes]
rs62484288	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62484291	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62484294	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62484295	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62484299	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62484300	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62485368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62485369	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62485370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62485372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62485377	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62485379	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62485383	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62485390	1.00[EUR][1000 genomes]
rs62485391	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62485452	0.84[EUR][1000 genomes]
rs62485453	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62487899	0.86[EUR][1000 genomes]
rs62487900	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62487901	0.80[ASN][1000 genomes]
rs62487902	0.80[ASN][1000 genomes]
rs62487904	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62487906	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62487911	0.83[ASN][1000 genomes]
rs62487912	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62487913	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62487914	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62487916	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62487918	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62487920	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62487921	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62487923	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71645962	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71645993	0.86[EUR][1000 genomes]
rs73492596	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7806794	0.82[EUR][1000 genomes]
rs7810757	0.86[EUR][1000 genomes];0.80[ASN][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	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
2	nsv518139	chr7:140512661-140622355	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv1029363	chr7:140567136-140594073	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
4	esv2761117	chr7:140582100-140594085	Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62485366	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140549000-140594400	Weak transcription	Fetal Thymus	thymus
2	chr7:140570600-140606000	Weak transcription	Fetal Intestine Small	intestine
3	chr7:140577000-140591000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:140577600-140598600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:140580400-140603200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:140582600-140599600	Weak transcription	Gastric	stomach
7	chr7:140586000-140590000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr7:140586000-140591600	Enhancers	K562	blood
9	chr7:140586000-140599400	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:140586000-140611600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:140586400-140592800	Weak transcription	Psoas Muscle	Psoas
12	chr7:140586400-140595000	Weak transcription	Primary B cells from cord blood	blood
13	chr7:140586400-140598600	Weak transcription	Brain Anterior Caudate	brain
14	chr7:140586400-140599600	Weak transcription	Adipose Nuclei	Adipose
15	chr7:140586400-140602000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr7:140586600-140589800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:140587000-140595800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:140587200-140591000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:140587200-140599400	Weak transcription	Brain Substantia Nigra	brain
20	chr7:140587400-140591600	Weak transcription	Primary T cells from cord blood	blood
21	chr7:140587400-140599600	Weak transcription	Fetal Lung	lung
22	chr7:140587600-140590200	Weak transcription	Colon Smooth Muscle	Colon
23	chr7:140587600-140596800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr7:140587800-140601800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr7:140588000-140593400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr7:140588000-140593600	Weak transcription	Lung	lung
27	chr7:140588200-140590200	Weak transcription	Fetal Heart	heart
28	chr7:140588200-140595600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:140588200-140598600	Weak transcription	A549	lung
30	chr7:140588400-140599000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:140588400-140599000	Weak transcription	Small Intestine	intestine
32	chr7:140588600-140591400	Weak transcription	Pancreas	Pancrea
33	chr7:140588600-140593400	Weak transcription	Right Atrium	heart
34	chr7:140588600-140599000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:140588600-140608400	Weak transcription	Ovary	ovary
36	chr7:140588800-140591000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:140589400-140591800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:140589400-140596400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr7:140589600-140589800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr7:140589600-140589800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr7:140589600-140589800	Enhancers	Liver	Liver
42	chr7:140589600-140589800	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr7:140589600-140589800	Enhancers	Fetal Intestine Large	intestine
44	chr7:140589600-140589800	Enhancers	Left Ventricle	heart
45	chr7:140589600-140589800	Enhancers	Right Ventricle	heart
46	chr7:140589600-140589800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr7:140589600-140589800	Enhancers	HepG2	liver
48	chr7:140589600-140590000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr7:140589600-140590000	Enhancers	GM12878-XiMat	blood
50	chr7:140589600-140590400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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