Variant report

Variant	rs1639675
Chromosome Location	chr7:140496563-140496564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140490975..140492582-chr7:140495499..140497183,2	MCF-7	breast:

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	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10247116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10251628	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10269699	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]
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];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267609	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267611	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267613	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267614	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267617	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267619	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];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267620	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267633	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1267636	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267639	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267640	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1267642	1.00[CEU][hapmap];0.91[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]
rs1267643	0.91[CHB][hapmap]
rs1267644	1.00[CEU][hapmap];0.91[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];1.00[ASN][1000 genomes]
rs1267649	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];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1270193	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1639678	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];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17161666	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs17161668	0.85[EUR][1000 genomes]
rs17161737	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17161767	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1733827	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]
rs1733832	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]
rs1812162	0.85[EUR][1000 genomes]
rs2245716	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2365098	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2535947	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2535951	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]
rs28577882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28579189	0.85[AMR][1000 genomes];0.96[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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6464121	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6464123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6464149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6464937	0.91[CHB][hapmap]
rs6464984	0.93[EUR][1000 genomes]
rs6949396	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][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];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6969779	0.87[EUR][1000 genomes]
rs6970121	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6975596	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73489531	0.87[EUR][1000 genomes]
rs73489562	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73491672	0.85[EUR][1000 genomes]
rs73491871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73497923	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73497924	0.89[ASN][1000 genomes]
rs73502717	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73502740	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73502747	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73502785	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73502799	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7787206	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7792746	0.91[CHB][hapmap]
rs7803697	0.92[CHB][hapmap]
rs9655610	0.85[AMR][1000 genomes];0.96[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
rs1639675	BRAF	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140404800-140517000	Weak transcription	Psoas Muscle	Psoas
2	chr7:140415000-140504400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:140415200-140506600	Weak transcription	Gastric	stomach
4	chr7:140441400-140504000	Weak transcription	NHLF	lung
5	chr7:140452400-140506200	Weak transcription	Pancreas	Pancrea
6	chr7:140465600-140500400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:140465800-140508600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:140467000-140505000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:140469000-140499600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:140469000-140503000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:140469000-140511200	Weak transcription	Right Ventricle	heart
12	chr7:140469200-140519600	Weak transcription	Aorta	Aorta
13	chr7:140470800-140504800	Weak transcription	NHEK	skin
14	chr7:140472800-140502000	Weak transcription	HMEC	breast
15	chr7:140473600-140513600	Weak transcription	Fetal Heart	heart
16	chr7:140474600-140511000	Weak transcription	Brain Substantia Nigra	brain
17	chr7:140475000-140509800	Weak transcription	Spleen	Spleen
18	chr7:140475000-140580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:140475600-140499600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:140477000-140500000	Weak transcription	Esophagus	oesophagus
21	chr7:140477200-140511200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:140477400-140497200	Weak transcription	A549	lung
23	chr7:140477400-140510800	Weak transcription	Ovary	ovary
24	chr7:140477800-140499600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:140479000-140505200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr7:140479600-140502800	Weak transcription	Brain Germinal Matrix	brain
27	chr7:140479600-140510800	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:140479600-140511200	Weak transcription	Lung	lung
29	chr7:140479600-140559000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:140479800-140502200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:140479800-140508200	Weak transcription	HSMMtube	muscle
32	chr7:140479800-140511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:140481000-140500200	Weak transcription	HUVEC	blood vessel
34	chr7:140483000-140510600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:140483800-140499800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:140486000-140499800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr7:140486400-140511000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr7:140486600-140503200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr7:140488000-140510600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr7:140488200-140511000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:140488600-140510600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr7:140488800-140503000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:140489200-140505000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr7:140489800-140496600	Strong transcription	Primary T cells from cord blood	blood
45	chr7:140490000-140501800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:140492200-140530600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:140492400-140496600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:140492600-140510600	Weak transcription	Colon Smooth Muscle	Colon
49	chr7:140493200-140500000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr7:140493200-140506600	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links