Variant report

Variant	rs6769762
Chromosome Location	chr3:135908178-135908179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:135907119..135909338-chr3:135913659..135917639,5	MCF-7	breast:
2	chr3:135905762..135909459-chr3:135968082..135970709,4	MCF-7	breast:
3	chr3:135902782..135906527-chr3:135906678..135909399,3	MCF-7	breast:
4	chr3:135897191..135900047-chr3:135906521..135908665,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114054	Chromatin interaction
ENSG00000174579	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10048942	0.84[CEU][hapmap]
rs10222451	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512990	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11720497	1.00[ASN][1000 genomes]
rs12330335	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068210	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079205	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13081671	0.89[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs13082532	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321220	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393786	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393787	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403763	0.89[CEU][hapmap];0.80[AMR][1000 genomes]
rs28509770	0.80[AMR][1000 genomes]
rs28519617	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535121	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669017	1.00[GIH][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34864445	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35320690	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35352346	0.89[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs35837273	1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs3905668	0.93[EUR][1000 genomes]
rs56398805	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439629	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67109185	0.81[EUR][1000 genomes]
rs67589653	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6767060	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775778	0.84[CEU][hapmap];0.84[MEX][hapmap]
rs6786582	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792630	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6793835	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6799056	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs6799320	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6799517	0.80[AMR][1000 genomes]
rs73222243	0.88[EUR][1000 genomes]
rs9653930	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9834966	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9837158	0.94[GIH][hapmap]
rs9844666	1.00[ASW][hapmap];0.94[GIH][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap]
rs9848926	0.89[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9870122	0.82[EUR][1000 genomes]
rs9880211	0.94[GIH][hapmap]
rs9881400	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6769762	MSL2	cis	cerebellum	SCAN
rs6769762	PPP2R3A	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135889400-135910400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr3:135890400-135909600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:135893600-135910400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:135897400-135909800	Enhancers	Primary T cells fromperipheralblood	blood
5	chr3:135897600-135909000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:135897600-135911000	Enhancers	Primary B cells from peripheral blood	blood
7	chr3:135898000-135910200	Weak transcription	HSMM	muscle
8	chr3:135898400-135909200	Weak transcription	Aorta	Aorta
9	chr3:135900800-135910400	Enhancers	Liver	Liver
10	chr3:135901000-135910400	Enhancers	HepG2	liver
11	chr3:135901600-135908600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:135903400-135911200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr3:135904400-135909800	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr3:135904400-135910400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr3:135904800-135908200	Enhancers	Primary B cells from cord blood	blood
16	chr3:135904800-135908200	Enhancers	NHEK	skin
17	chr3:135905000-135908200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:135905000-135908400	Enhancers	Small Intestine	intestine
19	chr3:135905000-135909000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr3:135905000-135909600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:135905200-135908200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:135905200-135908800	Enhancers	Fetal Thymus	thymus
23	chr3:135905400-135908400	Enhancers	Brain Germinal Matrix	brain
24	chr3:135905400-135908600	Enhancers	Primary T cells from cord blood	blood
25	chr3:135905400-135908800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:135905400-135909200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr3:135905400-135909200	Enhancers	Thymus	Thymus
28	chr3:135905600-135909800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:135905600-135910600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:135905800-135910400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:135906000-135909600	Enhancers	Psoas Muscle	Psoas
32	chr3:135906000-135909800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:135906000-135910600	Weak transcription	NH-A	brain
34	chr3:135906000-135911200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:135906200-135908600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr3:135906200-135908800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:135906200-135908800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:135906200-135909600	Weak transcription	HUVEC	blood vessel
39	chr3:135906200-135909800	Weak transcription	Fetal Kidney	kidney
40	chr3:135906200-135909800	Weak transcription	HMEC	breast
41	chr3:135906200-135910000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:135906200-135910400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:135906200-135910400	Weak transcription	NHDF-Ad	bronchial
44	chr3:135906400-135909200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr3:135906600-135908200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr3:135906800-135908200	Enhancers	Esophagus	oesophagus
47	chr3:135906800-135908200	Enhancers	Gastric	stomach
48	chr3:135907000-135909000	Enhancers	Placenta	Placenta
49	chr3:135907000-135909200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:135907000-135910400	Weak transcription	Fetal Intestine Large	intestine

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