Variant report

Variant	rs6967652
Chromosome Location	chr7:140576149-140576150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140574947..140577128-chr7:140708628..140711066,2	K562	blood:
2	chr7:140555946..140559478-chr7:140574386..140576522,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090263	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10241711	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10242534	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10247116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375245	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1267600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267609	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267611	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267613	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267614	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1267643	0.90[CHB][hapmap]
rs1267644	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1267649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1639678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1639679	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17161666	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs17161737	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17161750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1733832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs2364396	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2364397	0.90[CHB][hapmap]
rs2365097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs2968550	0.90[CHB][hapmap]
rs2968553	0.90[CHB][hapmap]
rs4727040	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4727041	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6464036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6464239	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
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]
rs6970121	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]
rs7803697	0.90[CHB][hapmap]
rs9655610	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351231	chr7:140390303-140588539	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv831158	chr7:140392222-140602315	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	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
4	nsv1024264	chr7:140539039-140576522	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv1027576	chr7:140539039-140576935	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	nsv1018200	chr7:140547011-140576522	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1022502	chr7:140547011-140576935	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv1017485	chr7:140560822-140576522	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv1026995	chr7:140560822-140576935	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	nsv1029363	chr7:140567136-140594073	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
11	nsv1015486	chr7:140567340-140581429	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6967652	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140475000-140580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:140547200-140582400	Weak transcription	Fetal Stomach	stomach
3	chr7:140548200-140576400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:140549000-140594400	Weak transcription	Fetal Thymus	thymus
5	chr7:140549400-140579000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:140560600-140576200	Weak transcription	NH-A	brain
7	chr7:140562000-140576600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:140563600-140576400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:140563600-140586000	Weak transcription	K562	blood
10	chr7:140566600-140576400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:140568000-140581200	Weak transcription	Pancreas	Pancrea
12	chr7:140568000-140586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:140568200-140577000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr7:140568400-140576400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:140568400-140580800	Weak transcription	HepG2	liver
16	chr7:140568600-140576800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:140570600-140576400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr7:140570600-140578400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:140570600-140580400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:140570600-140606000	Weak transcription	Fetal Intestine Small	intestine
21	chr7:140570800-140583000	Weak transcription	Primary B cells from cord blood	blood
22	chr7:140570800-140584200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:140571000-140580600	Weak transcription	Lung	lung
24	chr7:140571400-140576200	Weak transcription	Dnd41	blood
25	chr7:140571400-140576600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr7:140573600-140576800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:140573600-140577000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:140573600-140587800	Weak transcription	Left Ventricle	heart
29	chr7:140573800-140576200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr7:140573800-140581600	Weak transcription	Fetal Heart	heart
31	chr7:140574800-140576200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:140575200-140578600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr7:140575400-140576600	Enhancers	GM12878-XiMat	blood
34	chr7:140575400-140577000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:140575600-140577000	Enhancers	Primary T cells from cord blood	blood
36	chr7:140575600-140578000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr7:140575800-140576200	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr7:140575800-140576400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr7:140575800-140577000	Enhancers	HUVEC	blood vessel
40	chr7:140575800-140577600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr7:140575800-140577600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr7:140575800-140578600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr7:140576000-140576200	Enhancers	Adipose Nuclei	Adipose
44	chr7:140576000-140576200	Enhancers	Brain Angular Gyrus	brain
45	chr7:140576000-140576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr7:140576000-140577400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:140576000-140577600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:140576000-140577800	Enhancers	HUES48 Cell Line	embryonic stem cell

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