Variant report

Variant	rs6944039
Chromosome Location	chr7:140584017-140584018
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10234502	0.84[AMR][1000 genomes]
rs10235900	0.81[ASN][1000 genomes]
rs10240283	0.80[AMR][1000 genomes]
rs10240403	0.80[AMR][1000 genomes]
rs10244133	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10251380	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10251793	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10255130	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10255711	0.86[ASN][1000 genomes]
rs10258390	0.85[ASN][1000 genomes]
rs10261732	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10272940	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10281173	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10281508	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10282499	0.84[AMR][1000 genomes]
rs1042179	0.84[AMR][1000 genomes]
rs11981790	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1267602	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1267603	0.92[AMR][1000 genomes]
rs1267608	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1267612	0.81[ASN][1000 genomes]
rs1267615	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1267616	0.81[ASN][1000 genomes]
rs1267618	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1267621	0.81[ASN][1000 genomes]
rs1267623	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1267624	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1267625	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1267637	0.84[AMR][1000 genomes]
rs1267643	0.84[AMR][1000 genomes]
rs1267648	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1272419	0.84[AMR][1000 genomes]
rs17161762	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17161763	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2109307	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2109742	0.81[ASN][1000 genomes]
rs2535946	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2535948	0.82[AMR][1000 genomes]
rs2706774	0.86[AMR][1000 genomes]
rs2706775	0.81[ASN][1000 genomes]
rs4140846	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4726020	0.84[ASN][1000 genomes]
rs56797136	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57248447	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59055264	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62484301	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6464037	0.84[AMR][1000 genomes]
rs6944385	0.80[AMR][1000 genomes]
rs6947950	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6948703	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6950312	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6950946	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6951776	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6952601	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6953658	0.84[AMR][1000 genomes]
rs6954652	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6957490	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6961127	0.80[AMR][1000 genomes]
rs6964724	0.81[ASN][1000 genomes]
rs6964937	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6965532	0.83[ASN][1000 genomes]
rs6965559	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6966197	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7776491	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7791924	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7792984	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7793758	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7796827	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7798031	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7798324	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7800472	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7803738	0.84[AMR][1000 genomes]
rs9648715	0.80[AMR][1000 genomes]
rs9648716	0.80[AMR][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	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	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
5	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
rs6944039	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140549000-140594400	Weak transcription	Fetal Thymus	thymus
2	chr7:140563600-140586000	Weak transcription	K562	blood
3	chr7:140568000-140586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:140570600-140606000	Weak transcription	Fetal Intestine Small	intestine
5	chr7:140570800-140584200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr7:140573600-140587800	Weak transcription	Left Ventricle	heart
7	chr7:140576600-140585600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:140577000-140586800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr7:140577000-140591000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:140577400-140585600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:140577600-140586400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:140577600-140589600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:140577600-140598600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr7:140578600-140585600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:140578800-140586200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:140580400-140603200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:140581400-140585600	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:140581400-140587400	Weak transcription	Lung	lung
19	chr7:140581600-140585800	Weak transcription	Primary T cells from cord blood	blood
20	chr7:140581600-140586000	Weak transcription	Brain Angular Gyrus	brain
21	chr7:140581800-140585600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:140581800-140585600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr7:140581800-140585800	Weak transcription	Brain Anterior Caudate	brain
24	chr7:140581800-140586000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr7:140581800-140587200	Weak transcription	Fetal Heart	heart
26	chr7:140581800-140588000	Weak transcription	Pancreas	Pancrea
27	chr7:140582000-140585200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr7:140582600-140599600	Weak transcription	Gastric	stomach
29	chr7:140583600-140585800	Weak transcription	Primary B cells from cord blood	blood
30	chr7:140584000-140585200	Weak transcription	GM12878-XiMat	blood
31	chr7:140584000-140589600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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