Variant report

Variant	rs6964937
Chromosome Location	chr7:140609690-140609691
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140605056..140607360-chr7:140608917..140611801,3	K562	blood:
2	chr7:140609505..140611476-chr7:140622935..140624499,2	MCF-7	breast:
3	chr7:140588302..140590134-chr7:140608160..140610912,2	K562	blood:

Variant related genes	Relation type
ENSG00000157764	Chromatin interaction

Extended variants
information (count: 107 )
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];0.82[ASN][1000 genomes]
rs10232600	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10234502	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10235900	0.94[ASN][1000 genomes]
rs10240283	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10240403	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10244133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10251380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10251793	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10255130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10255711	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10258390	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10261732	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10263448	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10272940	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10281173	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10281508	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10282499	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1042179	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1092351	0.80[ASN][1000 genomes]
rs11768253	0.84[ASN][1000 genomes]
rs11769042	0.84[ASN][1000 genomes]
rs11981790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267602	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267603	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267608	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1267610	0.91[ASN][1000 genomes]
rs1267612	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267615	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267616	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267618	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267621	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267622	0.90[ASN][1000 genomes]
rs1267623	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267624	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267625	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267632	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267634	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267635	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267637	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1267643	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267645	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267646	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267647	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267648	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1272419	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17161762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17161763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2109307	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2109742	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2364399	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2535946	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2535948	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2706774	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2706775	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[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];0.87[ASN][1000 genomes]
rs3789806	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4140846	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4726020	0.91[ASN][1000 genomes]
rs56797136	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57248447	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59055264	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62484301	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6464037	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6464157	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6464159	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6944039	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6944385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6947950	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6948703	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6950312	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6950946	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6951776	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6952095	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6952601	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6953658	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6954652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6957490	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6957578	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6961127	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6962239	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6964724	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6965532	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6965559	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6966197	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6970893	0.80[AMR][1000 genomes]
rs7357151	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs765373	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7776491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7784523	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7785306	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7791924	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7792984	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7793758	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7796827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7798031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7798324	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7800472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7801086	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7803738	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9648715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9648716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs964942	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs986050	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6964937	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140586000-140611600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:140589800-140612000	Weak transcription	Fetal Intestine Large	intestine
3	chr7:140593800-140623200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:140594000-140610400	Weak transcription	Right Atrium	heart
5	chr7:140594000-140617200	Weak transcription	Lung	lung
6	chr7:140595800-140622400	Weak transcription	Aorta	Aorta
7	chr7:140597200-140623000	Weak transcription	Fetal Kidney	kidney
8	chr7:140599800-140612800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:140599800-140622000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:140600000-140622000	Weak transcription	Brain Anterior Caudate	brain
11	chr7:140600200-140612400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:140600800-140610400	Weak transcription	Left Ventricle	heart
13	chr7:140600800-140610400	Weak transcription	Psoas Muscle	Psoas
14	chr7:140600800-140612000	Weak transcription	Pancreas	Pancrea
15	chr7:140600800-140622600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr7:140602400-140612800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:140602400-140613600	Weak transcription	Brain Substantia Nigra	brain
18	chr7:140602600-140609800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:140603200-140610400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr7:140603600-140610200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:140603600-140613000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:140603600-140615800	Weak transcription	Primary T cells from cord blood	blood
23	chr7:140603800-140612000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:140604000-140622000	Weak transcription	Primary B cells from cord blood	blood
25	chr7:140604200-140611600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr7:140604200-140611800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:140604200-140613000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:140604200-140613000	Weak transcription	Fetal Lung	lung
29	chr7:140604200-140623000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:140604400-140611800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:140604400-140611800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:140605000-140618800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:140605200-140610600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr7:140606200-140609800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:140606200-140610400	Weak transcription	Fetal Intestine Small	intestine
36	chr7:140606200-140618200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:140607200-140621800	Weak transcription	Dnd41	blood
38	chr7:140607800-140612600	Weak transcription	Spleen	Spleen
39	chr7:140608000-140613000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:140608200-140611200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr7:140608400-140610200	Enhancers	Brain Hippocampus Middle	brain
42	chr7:140608400-140613000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:140608600-140609800	Weak transcription	K562	blood
44	chr7:140608600-140618000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:140608600-140618000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr7:140608600-140622000	Weak transcription	Adipose Nuclei	Adipose
47	chr7:140608800-140616000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr7:140609200-140610400	Weak transcription	Ovary	ovary
49	chr7:140609200-140623200	Weak transcription	Fetal Stomach	stomach
50	chr7:140609400-140611800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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