Variant report

Variant	rs62484299
Chromosome Location	chr7:140570824-140570825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140559226..140564238-chr7:140566941..140572115,8	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1009772	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10281975	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10488098	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11983228	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13438418	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1476868	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17622717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17623204	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17695341	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17695623	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17695707	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17695935	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17695995	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1968140	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41282721	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55720380	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55875248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56055746	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56115934	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56347011	0.95[EUR][1000 genomes]
rs56940988	0.82[ASN][1000 genomes]
rs57143942	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57620608	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57675404	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57725920	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57846481	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58901822	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59183598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59232128	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59477283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59816436	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60081231	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60187684	0.84[ASN][1000 genomes]
rs60251368	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61421775	0.82[ASN][1000 genomes]
rs62484288	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484295	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62484300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62485366	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62485368	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62485369	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62485370	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62485372	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62485377	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62485379	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62485383	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[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	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62487901	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62487902	0.82[ASN][1000 genomes]
rs62487904	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62487906	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62487911	0.85[ASN][1000 genomes]
rs62487912	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62487913	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62487914	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62487916	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62487918	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62487920	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487921	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62487923	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71645962	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71645993	0.86[EUR][1000 genomes]
rs73492596	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7806794	0.82[EUR][1000 genomes]
rs7810757	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1024264	chr7:140539039-140576522	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv1027576	chr7:140539039-140576935	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	nsv1018200	chr7:140547011-140576522	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1022502	chr7:140547011-140576935	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv1017485	chr7:140560822-140576522	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv1026995	chr7:140560822-140576935	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	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
11	nsv1015486	chr7:140567340-140581429	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
12	esv3417242	chr7:140570633-140571113	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62484299	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140475000-140580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:140527600-140573200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:140530600-140573200	Weak transcription	Gastric	stomach
4	chr7:140547000-140573200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:140547200-140573200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:140547200-140573400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:140547200-140582400	Weak transcription	Fetal Stomach	stomach
8	chr7:140547400-140572400	Weak transcription	Fetal Muscle Leg	muscle
9	chr7:140548200-140576400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:140549000-140594400	Weak transcription	Fetal Thymus	thymus
11	chr7:140549400-140579000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:140549600-140572400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr7:140552200-140573200	Weak transcription	Left Ventricle	heart
14	chr7:140557200-140574200	Weak transcription	Fetal Lung	lung
15	chr7:140560600-140576200	Weak transcription	NH-A	brain
16	chr7:140561400-140573000	Weak transcription	Right Atrium	heart
17	chr7:140562000-140576600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:140563600-140571000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:140563600-140573200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:140563600-140576400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:140563600-140586000	Weak transcription	K562	blood
22	chr7:140566600-140576400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:140566800-140571200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr7:140568000-140571000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr7:140568000-140574400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:140568000-140581200	Weak transcription	Pancreas	Pancrea
27	chr7:140568000-140586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:140568200-140576000	Weak transcription	Brain Angular Gyrus	brain
29	chr7:140568200-140577000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr7:140568400-140573200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:140568400-140576400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:140568400-140580800	Weak transcription	HepG2	liver
33	chr7:140568600-140576800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:140569600-140571200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr7:140569800-140571000	Enhancers	Primary B cells from peripheral blood	blood
36	chr7:140569800-140571000	Enhancers	Primary hematopoietic stem cells	blood
37	chr7:140570400-140571200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr7:140570400-140571400	Enhancers	Dnd41	blood
39	chr7:140570600-140571200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr7:140570600-140571400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr7:140570600-140576000	Weak transcription	Adipose Nuclei	Adipose
42	chr7:140570600-140576400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr7:140570600-140578400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr7:140570600-140580400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:140570600-140606000	Weak transcription	Fetal Intestine Small	intestine
46	chr7:140570800-140571000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr7:140570800-140571000	Enhancers	Lung	lung
48	chr7:140570800-140572800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:140570800-140573400	Weak transcription	GM12878-XiMat	blood
50	chr7:140570800-140574400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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