Variant report

Variant	rs6970121
Chromosome Location	chr7:140603375-140603376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140601410..140603492-chr7:140603943..140606432,3	K562	blood:
2	chr7:140602597..140604681-chr7:140623517..140626468,2	MCF-7	breast:
3	chr7:140596878..140600741-chr7:140602447..140607820,6	K562	blood:

Variant related genes	Relation type
ENSG00000157764	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10242534	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10247116	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10251628	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10269699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267600	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267601	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267606	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267609	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267611	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267613	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267614	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267617	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267619	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267633	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1267636	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267638	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267639	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267640	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267642	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267644	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267649	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1270193	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1639675	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1639678	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1639679	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17161737	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17161750	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17161767	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1733827	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1733832	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245716	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2365097	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2365098	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535947	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2535951	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28577882	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28579189	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464036	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6464121	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464123	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464149	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464984	0.80[EUR][1000 genomes]
rs6948377	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6949396	0.80[EUR][1000 genomes]
rs6962426	0.80[EUR][1000 genomes]
rs6967652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975596	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73489562	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73491871	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73497923	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73497924	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73497985	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73502717	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73502740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73502747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73502785	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73502799	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7787206	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9655610	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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
rs6970121	BRAF	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140570600-140606000	Weak transcription	Fetal Intestine Small	intestine
2	chr7:140586000-140611600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:140588600-140608400	Weak transcription	Ovary	ovary
4	chr7:140589800-140612000	Weak transcription	Fetal Intestine Large	intestine
5	chr7:140590800-140607600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:140591600-140603400	Weak transcription	K562	blood
7	chr7:140593800-140623200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr7:140594000-140610400	Weak transcription	Right Atrium	heart
9	chr7:140594000-140617200	Weak transcription	Lung	lung
10	chr7:140594600-140603600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:140595800-140622400	Weak transcription	Aorta	Aorta
12	chr7:140596000-140607400	Weak transcription	Spleen	Spleen
13	chr7:140597200-140623000	Weak transcription	Fetal Kidney	kidney
14	chr7:140598400-140605200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr7:140598600-140603600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:140599200-140603600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr7:140599800-140612800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:140599800-140622000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:140600000-140622000	Weak transcription	Brain Anterior Caudate	brain
20	chr7:140600200-140603400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:140600200-140612400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:140600800-140610400	Weak transcription	Left Ventricle	heart
23	chr7:140600800-140610400	Weak transcription	Psoas Muscle	Psoas
24	chr7:140600800-140612000	Weak transcription	Pancreas	Pancrea
25	chr7:140600800-140622600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr7:140601200-140603800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr7:140601400-140604000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr7:140601600-140603800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr7:140601600-140604200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:140601600-140604600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:140601800-140603600	Enhancers	Primary B cells from peripheral blood	blood
32	chr7:140602000-140603600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:140602400-140612800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr7:140602400-140613600	Weak transcription	Brain Substantia Nigra	brain
35	chr7:140602600-140604200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr7:140602600-140609800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr7:140602800-140603600	Enhancers	Primary T cells from cord blood	blood
38	chr7:140603000-140604200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:140603000-140604200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr7:140603000-140604200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr7:140603200-140603400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr7:140603200-140603400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:140603200-140603600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:140603200-140603800	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr7:140603200-140603800	ZNF genes & repeats	GM12878-XiMat	blood
46	chr7:140603200-140604000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
47	chr7:140603200-140604000	ZNF genes & repeats	Primary B cells from cord blood	blood
48	chr7:140603200-140604000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:140603200-140604200	ZNF genes & repeats	Fetal Lung	lung
50	chr7:140603200-140604400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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