Variant report

Variant	rs28529157
Chromosome Location	chr7:140614830-140614831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140606906..140609520-chr7:140613515..140616264,2	K562	blood:
2	chr7:140498910..140500950-chr7:140612218..140615111,2	K562	blood:
3	chr7:140612461..140615651-chr7:140623759..140625548,3	MCF-7	breast:
4	chr7:140609781..140612128-chr7:140612140..140615058,4	K562	blood:
5	chr7:140614023..140615840-chr7:140619443..140621784,2	MCF-7	breast:
6	chr7:140611711..140615434-chr7:140622283..140625319,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157764	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10232600	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10240283	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10240403	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10244133	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10251380	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10251793	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10255130	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10255711	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10261732	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10263448	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10272940	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10281173	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10281508	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11981790	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1267602	0.82[AMR][1000 genomes]
rs1267603	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1267618	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1267623	0.82[AMR][1000 genomes]
rs1267624	0.82[AMR][1000 genomes]
rs1267625	0.82[AMR][1000 genomes]
rs17161762	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17161763	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2109307	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2535946	0.82[AMR][1000 genomes]
rs2706774	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28605757	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56797136	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57248447	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59055264	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62484301	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6464157	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6464159	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6944385	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6947950	0.82[AMR][1000 genomes]
rs6948703	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6950312	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6950946	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6951776	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6952095	0.85[AMR][1000 genomes]
rs6952601	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6954652	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6957490	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6957578	0.86[AMR][1000 genomes]
rs6961127	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6962239	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6964937	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6965532	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6965559	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6966197	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs765373	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7776491	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7784523	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7785306	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7791924	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7792984	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7793758	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7796827	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7798031	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7798324	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7800472	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9648715	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9648716	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs964942	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[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
rs28529157	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140593800-140623200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr7:140594000-140617200	Weak transcription	Lung	lung
3	chr7:140595800-140622400	Weak transcription	Aorta	Aorta
4	chr7:140597200-140623000	Weak transcription	Fetal Kidney	kidney
5	chr7:140599800-140622000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:140600000-140622000	Weak transcription	Brain Anterior Caudate	brain
7	chr7:140600800-140622600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr7:140603600-140615800	Weak transcription	Primary T cells from cord blood	blood
9	chr7:140604000-140622000	Weak transcription	Primary B cells from cord blood	blood
10	chr7:140604200-140623000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:140605000-140618800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:140606200-140618200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:140607200-140621800	Weak transcription	Dnd41	blood
14	chr7:140608600-140618000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:140608600-140618000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:140608600-140622000	Weak transcription	Adipose Nuclei	Adipose
17	chr7:140608800-140616000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:140609200-140623200	Weak transcription	Fetal Stomach	stomach
19	chr7:140609800-140616600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:140610600-140617000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr7:140610800-140615600	Weak transcription	Ovary	ovary
22	chr7:140610800-140617000	Weak transcription	Left Ventricle	heart
23	chr7:140610800-140622600	Weak transcription	Right Atrium	heart
24	chr7:140610800-140623200	Weak transcription	Right Ventricle	heart
25	chr7:140611000-140615600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr7:140612000-140615600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr7:140612200-140616000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr7:140612200-140623400	Weak transcription	Gastric	stomach
29	chr7:140613000-140615600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:140613000-140622000	Weak transcription	Small Intestine	intestine
31	chr7:140613000-140622400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:140613200-140615000	Weak transcription	Fetal Lung	lung
33	chr7:140613200-140615600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:140613200-140615600	Weak transcription	Spleen	Spleen
35	chr7:140613200-140617200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:140613200-140618000	Weak transcription	Fetal Intestine Small	intestine
37	chr7:140613200-140618000	Weak transcription	Hela-S3	cervix
38	chr7:140613200-140622000	Weak transcription	Fetal Intestine Large	intestine
39	chr7:140613200-140623200	Weak transcription	Psoas Muscle	Psoas
40	chr7:140613600-140615600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:140613600-140623400	Weak transcription	Pancreas	Pancrea
42	chr7:140614000-140615000	Enhancers	Fetal Brain Male	brain
43	chr7:140614000-140620200	Weak transcription	Colon Smooth Muscle	Colon
44	chr7:140614200-140615400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:140614200-140615800	Weak transcription	GM12878-XiMat	blood
46	chr7:140614200-140616600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:140614200-140621800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:140614400-140615600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:140614400-140615600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr7:140614400-140615600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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