Variant report

Variant	rs62485377
Chromosome Location	chr7:140623286-140623287
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:140572911..140575551-chr7:140622620..140624458,2	MCF-7	breast:
2	chr7:140621971..140623569-chr7:140707032..140709391,2	MCF-7	breast:
3	chr7:140621726..140624133-chr7:141216889..141219173,2	K562	blood:
4	chr7:140532465..140534919-chr7:140622566..140624357,2	K562	blood:
5	chr7:140395267..140398426-chr7:140622802..140626309,6	K562	blood:
6	chr7:140621424..140625988-chr7:140712136..140716057,7	K562	blood:
7	chr7:140621424..140625828-chr7:140713150..140716057,6	K562	blood:
8	chr7:140395805..140398704-chr7:140623265..140626329,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000090263	Chromatin interaction
ENSG00000090266	Chromatin interaction
ENSG00000240889	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10281975	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10488098	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11983228	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13438418	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1476868	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17622717	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17623204	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17695341	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17695623	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17695707	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17695935	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17695995	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1968140	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2079827	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs246739	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs41282721	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55720380	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55875248	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56055746	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56115934	0.80[EUR][1000 genomes]
rs56347011	0.93[EUR][1000 genomes]
rs56940988	0.84[EUR][1000 genomes]
rs57143942	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57620608	0.84[EUR][1000 genomes]
rs57675404	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57846481	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58901822	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs59183598	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59232128	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59315265	0.84[ASN][1000 genomes]
rs59477283	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59816436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60081231	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60251368	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61421775	0.84[EUR][1000 genomes]
rs62484288	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62484291	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62484294	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62484295	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62484299	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62484300	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62485366	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62485368	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62485369	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62485370	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62485372	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62485379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62485383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62485390	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62485391	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62485452	0.82[EUR][1000 genomes]
rs62485453	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62487899	0.84[EUR][1000 genomes]
rs62487901	0.84[EUR][1000 genomes]
rs62487902	0.86[EUR][1000 genomes]
rs62487904	0.88[EUR][1000 genomes]
rs62487906	0.88[EUR][1000 genomes]
rs62487911	0.85[EUR][1000 genomes]
rs62487912	0.93[EUR][1000 genomes]
rs62487913	0.89[EUR][1000 genomes]
rs62487914	0.84[EUR][1000 genomes]
rs62487916	0.84[EUR][1000 genomes]
rs62487918	0.84[EUR][1000 genomes]
rs62487920	0.84[EUR][1000 genomes]
rs62487921	0.84[EUR][1000 genomes]
rs62487923	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71645962	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71645993	0.84[EUR][1000 genomes]
rs73492596	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7810757	0.93[EUR][1000 genomes];0.97[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	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
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62485377	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140612200-140623400	Weak transcription	Gastric	stomach
2	chr7:140613600-140623400	Weak transcription	Pancreas	Pancrea
3	chr7:140617400-140623400	Weak transcription	Left Ventricle	heart
4	chr7:140618400-140623400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:140618400-140623400	Weak transcription	Esophagus	oesophagus
6	chr7:140618400-140623400	Weak transcription	Lung	lung
7	chr7:140618400-140623400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:140619800-140623400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:140619800-140623400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr7:140620200-140623400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr7:140620200-140625400	Active TSS	GM12878-XiMat	blood
12	chr7:140620400-140623400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr7:140620400-140623400	Weak transcription	Ovary	ovary
14	chr7:140620800-140625200	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr7:140621600-140623400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:140621800-140623400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:140622000-140623400	Enhancers	Primary B cells from peripheral blood	blood
18	chr7:140622000-140623400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr7:140622000-140623600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:140622000-140625400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr7:140622200-140623800	Flanking Active TSS	Dnd41	blood
22	chr7:140622200-140625600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr7:140622400-140623400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr7:140622400-140623400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr7:140622400-140623800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:140622400-140624000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:140622600-140623400	Weak transcription	Small Intestine	intestine
28	chr7:140622600-140623800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:140622600-140624000	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr7:140622600-140624000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr7:140622600-140624000	Active TSS	Right Atrium	heart
32	chr7:140622600-140625200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:140622600-140625200	Active TSS	Fetal Intestine Large	intestine
34	chr7:140622600-140625400	Active TSS	Aorta	Aorta
35	chr7:140622600-140625400	Active TSS	Colonic Mucosa	Colon
36	chr7:140622600-140625400	Active TSS	Fetal Brain Female	brain
37	chr7:140622600-140625600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:140622800-140623400	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr7:140622800-140623400	Enhancers	Stomach Mucosa	stomach
40	chr7:140622800-140623600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr7:140622800-140624800	Active TSS	HMEC	breast
42	chr7:140622800-140625200	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr7:140622800-140625400	Active TSS	NHLF	lung
44	chr7:140622800-140625600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr7:140622800-140625600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr7:140622800-140625600	Active TSS	K562	blood
47	chr7:140623000-140623400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr7:140623000-140623400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr7:140623000-140623400	Active TSS	Fetal Brain Male	brain
50	chr7:140623000-140623400	Active TSS	HepG2	liver

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