Variant report

Variant	rs1812162
Chromosome Location	chr7:140413975-140413976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10241711	0.98[EUR][1000 genomes]
rs10242534	0.82[EUR][1000 genomes]
rs1046515	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12375245	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1267609	0.82[EUR][1000 genomes]
rs1267611	0.82[EUR][1000 genomes]
rs1267613	0.85[EUR][1000 genomes]
rs1267614	0.85[EUR][1000 genomes]
rs1267617	0.85[EUR][1000 genomes]
rs1267636	0.83[EUR][1000 genomes]
rs1267638	0.85[EUR][1000 genomes]
rs1267639	0.82[EUR][1000 genomes]
rs1267640	0.85[EUR][1000 genomes]
rs1267642	0.85[EUR][1000 genomes]
rs1267644	0.85[EUR][1000 genomes]
rs1267649	0.85[EUR][1000 genomes]
rs1270193	0.85[EUR][1000 genomes]
rs1639675	0.85[EUR][1000 genomes]
rs1639678	0.85[EUR][1000 genomes]
rs1639679	0.82[EUR][1000 genomes]
rs17161666	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17161668	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1733827	0.85[EUR][1000 genomes]
rs1733832	0.85[EUR][1000 genomes]
rs2245716	0.85[EUR][1000 genomes]
rs2364396	0.98[EUR][1000 genomes]
rs2364398	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2535951	0.83[EUR][1000 genomes]
rs28577882	0.85[EUR][1000 genomes]
rs4725799	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4727021	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4727036	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4727040	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4727041	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4727053	0.98[EUR][1000 genomes]
rs6464036	0.85[EUR][1000 genomes]
rs6464984	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6949396	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6962426	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6969779	0.98[EUR][1000 genomes]
rs73489531	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73489562	0.85[EUR][1000 genomes]
rs73491672	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73491871	0.85[EUR][1000 genomes]
rs73505647	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv869260	chr7:140404835-140542905	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1015269	chr7:140412464-140458821	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1812162	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140398000-140419400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr7:140398000-140466600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:140398200-140473800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:140398200-140492600	Weak transcription	Colonic Mucosa	Colon
5	chr7:140398400-140422000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:140398400-140432200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:140398600-140414800	Weak transcription	Small Intestine	intestine
8	chr7:140398600-140459400	Weak transcription	Brain Germinal Matrix	brain
9	chr7:140398600-140491800	Weak transcription	Fetal Brain Male	brain
10	chr7:140399400-140414200	Weak transcription	Gastric	stomach
11	chr7:140399400-140468200	Weak transcription	Right Ventricle	heart
12	chr7:140399600-140443800	Weak transcription	Fetal Heart	heart
13	chr7:140400000-140474000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:140404400-140452400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:140404800-140414200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:140404800-140419600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr7:140404800-140427600	Weak transcription	HSMMtube	muscle
18	chr7:140404800-140489000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:140404800-140517000	Weak transcription	Psoas Muscle	Psoas
20	chr7:140405200-140470800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr7:140405600-140472200	Weak transcription	Brain Substantia Nigra	brain
22	chr7:140406000-140414200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:140406200-140418800	Weak transcription	Fetal Kidney	kidney
24	chr7:140406600-140414000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:140406600-140472800	Weak transcription	Hela-S3	cervix
26	chr7:140407000-140414200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:140407000-140425600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:140407000-140425600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:140407000-140427400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr7:140407000-140427600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:140407000-140428800	Weak transcription	NHLF	lung
32	chr7:140407000-140454200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr7:140407000-140466800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:140407200-140414000	Weak transcription	Primary B cells from cord blood	blood
35	chr7:140407200-140414000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr7:140407200-140414000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:140407200-140414000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr7:140407200-140414200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:140407200-140414200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:140407200-140414200	Weak transcription	Primary T cells from cord blood	blood
41	chr7:140407200-140414200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:140407200-140414200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:140407200-140414200	Weak transcription	Aorta	Aorta
44	chr7:140407200-140414200	Weak transcription	Liver	Liver
45	chr7:140407200-140414200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr7:140407200-140414200	Weak transcription	Fetal Intestine Small	intestine
47	chr7:140407200-140414200	Weak transcription	Lung	lung
48	chr7:140407200-140414200	Weak transcription	K562	blood
49	chr7:140407200-140414400	Weak transcription	Fetal Brain Female	brain
50	chr7:140407200-140414600	Weak transcription	Placenta	Placenta

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