Variant report

Variant	rs1267639
Chromosome Location	chr7:140473772-140473773
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140473570..140476924-chr7:140480357..140483347,3	K562	blood:

Variant related genes	Relation type
ENSG00000157764	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10241711	0.84[EUR][1000 genomes]
rs10242534	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10247116	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10251628	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10269699	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1046515	0.82[EUR][1000 genomes]
rs12375245	0.82[EUR][1000 genomes]
rs1267600	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267601	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267606	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267609	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267611	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267613	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267614	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267617	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267619	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1267620	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1267633	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1267636	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267640	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267642	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267644	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267649	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1270193	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1639675	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1639678	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1639679	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17161666	0.82[EUR][1000 genomes]
rs17161668	0.82[EUR][1000 genomes]
rs17161737	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17161750	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17161767	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1733827	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1733832	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1812162	0.82[EUR][1000 genomes]
rs2245716	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2364396	0.84[EUR][1000 genomes]
rs2364398	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2365097	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2365098	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2535947	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535951	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28577882	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28579189	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4725799	0.81[EUR][1000 genomes]
rs4727021	0.81[EUR][1000 genomes]
rs4727036	0.82[EUR][1000 genomes]
rs4727040	0.81[EUR][1000 genomes]
rs4727041	0.82[EUR][1000 genomes]
rs4727053	0.84[EUR][1000 genomes]
rs6464036	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6464121	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6464123	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6464149	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6464984	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6949396	0.90[EUR][1000 genomes]
rs6962426	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6967652	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6969779	0.84[EUR][1000 genomes]
rs6970121	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6975596	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73489531	0.84[EUR][1000 genomes]
rs73489562	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73491672	0.82[EUR][1000 genomes]
rs73491871	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73497923	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73497924	0.88[ASN][1000 genomes]
rs73502717	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73502740	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73502747	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73502785	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73502799	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7787206	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9655610	0.85[AMR][1000 genomes];0.89[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	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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1267639	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	chr7:140398200-140473800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:140398200-140492600	Weak transcription	Colonic Mucosa	Colon
3	chr7:140398600-140491800	Weak transcription	Fetal Brain Male	brain
4	chr7:140400000-140474000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:140404800-140489000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:140404800-140517000	Weak transcription	Psoas Muscle	Psoas
7	chr7:140415000-140504400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:140415200-140506600	Weak transcription	Gastric	stomach
9	chr7:140421800-140474000	Weak transcription	Brain Angular Gyrus	brain
10	chr7:140424400-140476600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr7:140428200-140489400	Weak transcription	Small Intestine	intestine
12	chr7:140428600-140476600	Weak transcription	NHDF-Ad	bronchial
13	chr7:140431200-140474200	Weak transcription	Esophagus	oesophagus
14	chr7:140438400-140482400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr7:140439600-140474800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:140440400-140476400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:140440600-140492600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:140441400-140504000	Weak transcription	NHLF	lung
19	chr7:140444200-140485600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr7:140446200-140474800	Weak transcription	HSMM	muscle
21	chr7:140449200-140474600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr7:140452400-140506200	Weak transcription	Pancreas	Pancrea
23	chr7:140454000-140476000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:140454200-140474400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:140455800-140475000	Weak transcription	GM12878-XiMat	blood
26	chr7:140458200-140478600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:140460000-140478600	Weak transcription	Brain Germinal Matrix	brain
28	chr7:140462800-140475600	Weak transcription	HUVEC	blood vessel
29	chr7:140463600-140474200	Weak transcription	Osteobl	bone
30	chr7:140464800-140495600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr7:140465600-140500400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr7:140465800-140508600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:140466400-140479600	Strong transcription	Primary T cells from cord blood	blood
34	chr7:140466400-140484800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr7:140466400-140487600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:140466600-140484400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr7:140466600-140494600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr7:140467000-140474200	Weak transcription	Thymus	Thymus
39	chr7:140467000-140475600	Weak transcription	A549	lung
40	chr7:140467000-140478800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:140467000-140505000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:140467200-140484000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr7:140467600-140474200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr7:140467800-140474400	Weak transcription	Brain Hippocampus Middle	brain
45	chr7:140467800-140475400	Weak transcription	Fetal Kidney	kidney
46	chr7:140468000-140486000	Weak transcription	HepG2	liver
47	chr7:140468200-140474600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:140468200-140478000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr7:140468800-140474200	Weak transcription	Spleen	Spleen
50	chr7:140468800-140477200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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