Variant report

Variant	rs1639678
Chromosome Location	chr7:140509923-140509924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140508535..140511322-chr7:140704600..140707127,2	MCF-7	breast:
2	chr7:140508977..140512218-chr7:140712062..140714684,5	MCF-7	breast:
3	chr7:140509634..140513018-chr7:140622875..140626289,4	MCF-7	breast:
4	chr7:140509026..140511710-chr7:140712128..140713632,2	K562	blood:
5	chr7:140508931..140513755-chr7:140712128..140716834,7	K562	blood:

Variant related genes	Relation type
ENSG00000090263	Chromatin interaction
ENSG00000157764	Chromatin interaction
ENSG00000273081	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10241711	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10242534	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10247116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10251628	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10269699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1046515	0.85[EUR][1000 genomes]
rs1140034	0.91[CHB][hapmap]
rs12375245	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1267600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267609	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267611	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267613	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267614	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267617	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267620	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267633	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267636	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267639	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267640	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267642	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267643	0.91[CHB][hapmap]
rs1267644	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1270193	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1639675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1639679	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161666	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs17161668	0.85[EUR][1000 genomes]
rs17161737	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17161750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17161767	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1733827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1733832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812162	0.85[EUR][1000 genomes]
rs2245716	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2364393	0.91[CHB][hapmap]
rs2364394	0.91[CHB][hapmap]
rs2364396	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2364397	0.92[CHB][hapmap]
rs2364398	0.92[EUR][1000 genomes]
rs2365097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2365098	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2535947	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28577882	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28579189	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2968550	0.92[CHB][hapmap]
rs2968553	0.92[CHB][hapmap]
rs2968559	0.91[CHB][hapmap]
rs4725799	0.84[EUR][1000 genomes]
rs4727011	0.91[CHB][hapmap]
rs4727021	0.84[EUR][1000 genomes]
rs4727036	0.85[EUR][1000 genomes]
rs4727040	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4727041	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4727053	0.87[EUR][1000 genomes]
rs6464036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6464121	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6464123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6464149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6464937	0.91[CHB][hapmap]
rs6464984	0.93[EUR][1000 genomes]
rs6949396	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6962426	0.93[EUR][1000 genomes]
rs6967652	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]
rs6969779	0.87[EUR][1000 genomes]
rs6970121	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6975596	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73489531	0.87[EUR][1000 genomes]
rs73489562	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73491672	0.85[EUR][1000 genomes]
rs73491871	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73497923	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs73497924	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73502717	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73502740	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73502747	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73502785	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73502799	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7787206	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7792746	0.91[CHB][hapmap]
rs7803697	0.92[CHB][hapmap]
rs9655610	0.81[AMR][1000 genomes];0.94[ASN][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	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	nsv869260	chr7:140404835-140542905	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1639678	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140404800-140517000	Weak transcription	Psoas Muscle	Psoas
2	chr7:140469000-140511200	Weak transcription	Right Ventricle	heart
3	chr7:140469200-140519600	Weak transcription	Aorta	Aorta
4	chr7:140473600-140513600	Weak transcription	Fetal Heart	heart
5	chr7:140474600-140511000	Weak transcription	Brain Substantia Nigra	brain
6	chr7:140475000-140580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:140477200-140511200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:140477400-140510800	Weak transcription	Ovary	ovary
9	chr7:140479600-140510800	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:140479600-140511200	Weak transcription	Lung	lung
11	chr7:140479600-140559000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr7:140479800-140511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:140483000-140510600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr7:140486400-140511000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr7:140488000-140510600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr7:140488200-140511000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:140488600-140510600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:140492200-140530600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:140492600-140510600	Weak transcription	Colon Smooth Muscle	Colon
20	chr7:140493600-140536200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:140493800-140510400	Weak transcription	HepG2	liver
22	chr7:140493800-140551800	Weak transcription	Left Ventricle	heart
23	chr7:140494400-140520400	Weak transcription	Fetal Stomach	stomach
24	chr7:140494400-140545400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:140494400-140555600	Weak transcription	Hela-S3	cervix
26	chr7:140494600-140517200	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:140498000-140548600	Weak transcription	A549	lung
28	chr7:140499200-140530400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr7:140500200-140511000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:140500200-140517400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:140500200-140530400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:140500200-140533800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr7:140500400-140510200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr7:140500400-140510600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:140500400-140511000	Weak transcription	Fetal Kidney	kidney
36	chr7:140500400-140511200	Weak transcription	Placenta	Placenta
37	chr7:140500400-140517400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:140500400-140517400	Weak transcription	HSMM	muscle
39	chr7:140500400-140526800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr7:140500400-140529400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr7:140500400-140533800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr7:140500400-140534000	Weak transcription	Fetal Thymus	thymus
43	chr7:140500400-140545600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:140500400-140548800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr7:140500800-140511400	Weak transcription	NH-A	brain
46	chr7:140500800-140526600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr7:140501000-140517000	Weak transcription	Fetal Lung	lung
48	chr7:140501400-140510400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr7:140501400-140511000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:140501600-140510200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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