Variant report

Variant	rs1267620
Chromosome Location	chr7:140563516-140563517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140555134..140561473-chr7:140561764..140565765,7	K562	blood:
2	chr7:140559226..140564238-chr7:140566941..140572115,8	K562	blood:
3	chr7:140561409..140564479-chr7:140621368..140624778,3	K562	blood:
4	chr7:140560224..140564238-chr7:140566941..140570656,4	K562	blood:

Variant related genes	Relation type
ENSG00000157764	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10242534	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10247116	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10251628	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10269699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267600	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267601	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267606	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267609	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267611	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267613	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267614	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267617	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267619	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267633	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1267636	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267638	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1267639	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1267640	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1267642	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267644	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267649	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1270193	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1639675	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1639678	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1639679	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17161737	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17161750	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161767	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1733827	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1733832	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2245716	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365097	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2365098	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2535947	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2535951	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28577882	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28579189	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6464036	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6464121	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6464123	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6464149	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6464984	0.80[EUR][1000 genomes]
rs6948377	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6949396	0.80[EUR][1000 genomes]
rs6962426	0.80[EUR][1000 genomes]
rs6967652	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6970121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6975596	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73489562	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73491871	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73497923	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73497924	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73502717	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73502740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73502747	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73502785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73502799	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787206	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9655610	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1030989	chr7:140547011-140569821	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	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
8	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
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1267620	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 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	chr7:140524400-140567800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:140525200-140567400	Weak transcription	Right Ventricle	heart
4	chr7:140527600-140573200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:140530400-140564800	Weak transcription	Aorta	Aorta
6	chr7:140530600-140573200	Weak transcription	Gastric	stomach
7	chr7:140534600-140567600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:140534600-140570200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr7:140546000-140567600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr7:140546600-140567200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:140547000-140564600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr7:140547000-140573200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:140547200-140567600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:140547200-140567600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:140547200-140573200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:140547200-140573400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr7:140547200-140582400	Weak transcription	Fetal Stomach	stomach
18	chr7:140547400-140572400	Weak transcription	Fetal Muscle Leg	muscle
19	chr7:140547800-140567600	Weak transcription	Thymus	Thymus
20	chr7:140548000-140564600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr7:140548200-140563600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr7:140548200-140576400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:140549000-140564000	Weak transcription	Fetal Brain Female	brain
24	chr7:140549000-140567600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr7:140549000-140567600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr7:140549000-140567600	Weak transcription	Liver	Liver
27	chr7:140549000-140594400	Weak transcription	Fetal Thymus	thymus
28	chr7:140549200-140563800	Weak transcription	Dnd41	blood
29	chr7:140549200-140567600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:140549200-140569000	Weak transcription	Fetal Intestine Large	intestine
31	chr7:140549200-140569800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:140549400-140579000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:140549600-140572400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr7:140552200-140567600	Weak transcription	Psoas Muscle	Psoas
35	chr7:140552200-140573200	Weak transcription	Left Ventricle	heart
36	chr7:140557000-140567600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr7:140557200-140563800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:140557200-140574200	Weak transcription	Fetal Lung	lung
39	chr7:140557400-140567200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr7:140557400-140567600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr7:140560600-140576200	Weak transcription	NH-A	brain
42	chr7:140561000-140566800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr7:140561400-140573000	Weak transcription	Right Atrium	heart
44	chr7:140562000-140567400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr7:140562000-140567600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr7:140562000-140576600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr7:140562800-140563600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:140563000-140566200	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr7:140563200-140564800	Strong transcription	Primary T cells from cord blood	blood
50	chr7:140563400-140563600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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