Variant report

Variant	rs56347011
Chromosome Location	chr7:140625744-140625745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr7:140624848-140625765	K562	blood:	n/a	n/a
2	JUND	chr7:140622356-140625981	SK-N-SH	brain:	n/a	chr7:140623694-140623703 chr7:140624751-140624760 chr7:140624840-140624849 chr7:140623251-140623263 chr7:140624822-140624831
3	CREB1	chr7:140623277-140625770	K562	blood:	n/a	chr7:140624820-140624833
4	JUN	chr7:140624568-140625909	K562	blood:	n/a	chr7:140624836-140624849 chr7:140624751-140624760 chr7:140624821-140624834 chr7:140624840-140624849 chr7:140624822-140624831

No.	Distal block	Cell Line	Cell type
1	chr7:140625504..140628313-chr7:140642636..140644756,2	K562	blood:
2	chr7:140625343..140628260-chr7:140713839..140715821,2	MCF-7	breast:
3	chr7:140624883..140626746-chr7:140635141..140637023,2	K562	blood:
4	chr7:140395267..140398426-chr7:140622802..140626309,6	K562	blood:
5	chr7:140621424..140625988-chr7:140712136..140716057,7	K562	blood:
6	chr7:140621424..140625828-chr7:140713150..140716057,6	K562	blood:
7	chr7:140395805..140398704-chr7:140623265..140626329,4	K562	blood:

Variant related genes	Relation type
BRAF	TF binding region
ENSG00000240889	Chromatin interaction
ENSG00000090266	Chromatin interaction
ENSG00000090263	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1009772	0.86[EUR][1000 genomes]
rs10240888	0.81[EUR][1000 genomes]
rs10281975	0.91[EUR][1000 genomes]
rs10488098	0.95[EUR][1000 genomes]
rs11977567	1.00[ASN][1000 genomes]
rs11983228	0.89[EUR][1000 genomes]
rs13438418	0.91[EUR][1000 genomes]
rs13438609	0.82[EUR][1000 genomes]
rs1476868	0.95[EUR][1000 genomes]
rs17622717	0.95[EUR][1000 genomes]
rs17623204	0.95[EUR][1000 genomes]
rs17695341	0.95[EUR][1000 genomes]
rs17695623	0.95[EUR][1000 genomes]
rs17695707	0.93[EUR][1000 genomes]
rs17695935	0.89[EUR][1000 genomes]
rs17695995	0.95[EUR][1000 genomes]
rs1968140	0.90[EUR][1000 genomes]
rs2079827	0.88[EUR][1000 genomes]
rs246739	0.88[EUR][1000 genomes]
rs2907951	1.00[ASN][1000 genomes]
rs2907952	1.00[ASN][1000 genomes]
rs2930316	1.00[ASN][1000 genomes]
rs2930317	1.00[ASN][1000 genomes]
rs2930323	1.00[ASN][1000 genomes]
rs2930325	1.00[ASN][1000 genomes]
rs2968546	1.00[ASN][1000 genomes]
rs2968554	1.00[ASN][1000 genomes]
rs38715	0.81[EUR][1000 genomes]
rs38717	0.81[EUR][1000 genomes]
rs38718	0.81[EUR][1000 genomes]
rs38719	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs38720	0.81[EUR][1000 genomes]
rs38722	0.81[EUR][1000 genomes]
rs38723	0.81[EUR][1000 genomes]
rs38726	0.81[EUR][1000 genomes]
rs38730	0.81[EUR][1000 genomes]
rs38731	0.81[EUR][1000 genomes]
rs41282721	0.90[EUR][1000 genomes]
rs55720380	0.95[EUR][1000 genomes]
rs55875248	0.95[EUR][1000 genomes]
rs56055746	0.90[EUR][1000 genomes]
rs56115934	0.86[EUR][1000 genomes]
rs56940988	0.82[EUR][1000 genomes]
rs57143942	0.91[EUR][1000 genomes]
rs57620608	0.90[EUR][1000 genomes]
rs57675404	0.95[EUR][1000 genomes]
rs57846481	0.95[EUR][1000 genomes]
rs58901822	0.88[EUR][1000 genomes]
rs59183598	0.95[EUR][1000 genomes]
rs59232128	0.95[EUR][1000 genomes]
rs59477283	0.95[EUR][1000 genomes]
rs59816436	0.95[EUR][1000 genomes]
rs60081231	0.95[EUR][1000 genomes]
rs60251368	0.95[EUR][1000 genomes]
rs61421775	0.82[EUR][1000 genomes]
rs62484288	0.95[EUR][1000 genomes]
rs62484291	0.95[EUR][1000 genomes]
rs62484294	0.95[EUR][1000 genomes]
rs62484295	0.93[EUR][1000 genomes]
rs62484299	0.95[EUR][1000 genomes]
rs62484300	0.95[EUR][1000 genomes]
rs62485366	0.95[EUR][1000 genomes]
rs62485368	0.95[EUR][1000 genomes]
rs62485369	0.91[EUR][1000 genomes]
rs62485370	0.95[EUR][1000 genomes]
rs62485372	0.95[EUR][1000 genomes]
rs62485377	0.93[EUR][1000 genomes]
rs62485379	0.93[EUR][1000 genomes]
rs62485383	0.95[EUR][1000 genomes]
rs62485390	0.95[EUR][1000 genomes]
rs62485391	0.93[EUR][1000 genomes]
rs62485451	0.81[EUR][1000 genomes]
rs62485452	0.88[EUR][1000 genomes]
rs62485453	0.88[EUR][1000 genomes]
rs62487899	0.90[EUR][1000 genomes]
rs62487900	0.86[EUR][1000 genomes]
rs62487901	0.82[EUR][1000 genomes]
rs62487902	0.84[EUR][1000 genomes]
rs62487904	0.86[EUR][1000 genomes]
rs62487906	0.86[EUR][1000 genomes]
rs62487911	0.82[EUR][1000 genomes]
rs62487912	0.90[EUR][1000 genomes]
rs62487913	0.86[EUR][1000 genomes]
rs62487914	0.90[EUR][1000 genomes]
rs62487916	0.90[EUR][1000 genomes]
rs62487918	0.90[EUR][1000 genomes]
rs62487920	0.90[EUR][1000 genomes]
rs62487921	0.90[EUR][1000 genomes]
rs62487923	0.90[EUR][1000 genomes]
rs71645962	0.90[EUR][1000 genomes]
rs71645993	0.90[EUR][1000 genomes]
rs73492596	0.87[EUR][1000 genomes]
rs7810757	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3422481	chr7:140623508-140626056	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56347011	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140625000-140626000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr7:140625200-140627200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:140625200-140627400	Weak transcription	Small Intestine	intestine
4	chr7:140625400-140625800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:140625400-140625800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:140625400-140625800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr7:140625400-140625800	Weak transcription	Aorta	Aorta
8	chr7:140625400-140625800	Enhancers	Fetal Lung	lung
9	chr7:140625400-140625800	Enhancers	HepG2	liver
10	chr7:140625400-140625800	Enhancers	Osteobl	bone
11	chr7:140625400-140626000	Enhancers	Primary B cells from peripheral blood	blood
12	chr7:140625400-140627000	Enhancers	Fetal Heart	heart
13	chr7:140625400-140628000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:140625400-140628000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr7:140625600-140625800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr7:140625600-140625800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr7:140625600-140625800	Enhancers	Brain Anterior Caudate	brain
18	chr7:140625600-140625800	Enhancers	Brain Germinal Matrix	brain
19	chr7:140625600-140625800	Enhancers	Fetal Intestine Large	intestine
20	chr7:140625600-140625800	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr7:140625600-140625800	Enhancers	Stomach Smooth Muscle	stomach
22	chr7:140625600-140626000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:140625600-140626000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:140625600-140626000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:140625600-140626000	Enhancers	Psoas Muscle	Psoas
26	chr7:140625600-140626400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr7:140625600-140626600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr7:140625600-140628000	Weak transcription	NHEK	skin
29	chr7:140625600-140628200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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