Variant report

Variant	rs11981790
Chromosome Location	chr7:140588384-140588385
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140559633..140561782-chr7:140587885..140590240,2	MCF-7	breast:
2	chr7:140586780..140588546-chr7:140616185..140618447,2	K562	blood:
3	chr7:140585371..140588493-chr7:140589347..140593837,4	K562	blood:
4	chr7:140588302..140590134-chr7:140608160..140610912,2	K562	blood:
5	chr7:140588144..140589724-chr7:140618968..140621680,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10232557	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10232600	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10234502	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10235900	0.95[ASN][1000 genomes]
rs10240283	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10240403	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10244133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10251380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10251793	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10255130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10255711	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10258390	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10261732	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10263448	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10272940	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10281173	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10281508	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10282499	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1042179	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1092351	0.82[ASN][1000 genomes]
rs11768253	0.85[ASN][1000 genomes]
rs11769042	0.85[ASN][1000 genomes]
rs1267602	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1267603	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267608	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1267610	0.92[ASN][1000 genomes]
rs1267612	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1267615	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1267616	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1267618	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1267621	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1267622	0.91[ASN][1000 genomes]
rs1267623	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1267624	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1267625	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1267632	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267634	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267635	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267637	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1267643	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267645	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267646	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267647	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267648	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1272419	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17161762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17161763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2109307	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2109742	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2364399	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2535946	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2535948	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2706774	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2706775	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28529157	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28605757	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3789806	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4140846	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4726020	0.92[ASN][1000 genomes]
rs56797136	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57248447	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59055264	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62484301	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6464037	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6464157	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6464159	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6944039	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6944385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6947950	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6948703	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6950312	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6950946	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6951776	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6952095	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6952601	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6953658	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6954652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6957490	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6957578	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6961127	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6962239	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6964724	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6964937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6965532	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6965559	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6966197	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6970893	0.80[AMR][1000 genomes]
rs7357151	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs765373	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7776491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7784523	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7785306	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7791924	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7792984	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7793758	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7796827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7798031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7798324	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7800472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7801086	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7803738	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9648715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9648716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs964942	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs986050	0.83[EUR][1000 genomes];0.89[ASN][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
rs11981790	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140549000-140594400	Weak transcription	Fetal Thymus	thymus
2	chr7:140570600-140606000	Weak transcription	Fetal Intestine Small	intestine
3	chr7:140577000-140591000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr7:140577600-140589600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:140577600-140598600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:140580400-140603200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr7:140582600-140599600	Weak transcription	Gastric	stomach
8	chr7:140584000-140589600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:140585200-140589000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr7:140586000-140590000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr7:140586000-140591600	Enhancers	K562	blood
12	chr7:140586000-140599400	Weak transcription	Brain Hippocampus Middle	brain
13	chr7:140586000-140611600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:140586400-140592800	Weak transcription	Psoas Muscle	Psoas
15	chr7:140586400-140595000	Weak transcription	Primary B cells from cord blood	blood
16	chr7:140586400-140598600	Weak transcription	Brain Anterior Caudate	brain
17	chr7:140586400-140599600	Weak transcription	Adipose Nuclei	Adipose
18	chr7:140586400-140602000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:140586600-140589800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:140587000-140588600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:140587000-140589600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:140587000-140595800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr7:140587200-140588400	Enhancers	Hela-S3	cervix
24	chr7:140587200-140588800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:140587200-140589600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:140587200-140591000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:140587200-140599400	Weak transcription	Brain Substantia Nigra	brain
28	chr7:140587400-140588400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr7:140587400-140589400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:140587400-140589600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr7:140587400-140589600	Weak transcription	GM12878-XiMat	blood
32	chr7:140587400-140591600	Weak transcription	Primary T cells from cord blood	blood
33	chr7:140587400-140599600	Weak transcription	Fetal Lung	lung
34	chr7:140587600-140588600	Enhancers	Ovary	ovary
35	chr7:140587600-140589400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr7:140587600-140589600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:140587600-140589600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:140587600-140590200	Weak transcription	Colon Smooth Muscle	Colon
39	chr7:140587600-140596800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:140587800-140588600	Enhancers	Right Atrium	heart
41	chr7:140587800-140588800	Enhancers	Left Ventricle	heart
42	chr7:140587800-140589600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:140587800-140601800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr7:140588000-140588400	Enhancers	HepG2	liver
45	chr7:140588000-140588600	Enhancers	Pancreas	Pancrea
46	chr7:140588000-140593400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr7:140588000-140593600	Weak transcription	Lung	lung
48	chr7:140588200-140588400	Enhancers	Small Intestine	intestine
49	chr7:140588200-140589600	Weak transcription	Right Ventricle	heart
50	chr7:140588200-140590200	Weak transcription	Fetal Heart	heart

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