Variant report

Variant	rs603035
Chromosome Location	chr8:61518273-61518274
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	chr8:61511100..61513643-chr8:61515847..61518764,3	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10098769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10102740	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10808709	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10957147	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10957150	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1120591	1.00[CEU][hapmap]
rs11996592	0.96[CEU][hapmap]
rs12681129	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1319104	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1319105	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2056415	0.93[CEU][hapmap]
rs2272620	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2272621	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2326560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2326561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2326562	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2326568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2326569	0.93[CEU][hapmap]
rs2326570	0.93[CEU][hapmap]
rs2326571	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2625441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2875967	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2875968	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2875973	1.00[CEU][hapmap]
rs2875974	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2930040	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2946154	0.93[CEU][hapmap]
rs2981277	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs3735825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs3735826	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs41420549	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs595255	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs601778	0.81[JPT][hapmap]
rs615031	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs617834	0.93[CEU][hapmap]
rs625850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs625979	0.80[JPT][hapmap]
rs629268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs652422	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs659118	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs669599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs671576	0.81[JPT][hapmap]
rs687978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6987084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6995515	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7000166	0.93[CEU][hapmap]
rs7013249	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7815543	0.93[CEU][hapmap]
rs7824045	1.00[CEU][hapmap]
rs7827453	1.00[CEU][hapmap]
rs7829359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7839516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7842586	1.00[CEU][hapmap]
rs9298039	0.96[CEU][hapmap]
rs9643523	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530383	chr8:61431756-61605551	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv870164	chr8:61484657-61529482	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv6218	chr8:61485410-61530933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1796952	chr8:61492893-61531418	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv831335	chr8:61497540-61688992	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs603035	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs603035	RAB2A	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61481000-61527400	Weak transcription	Psoas Muscle	Psoas
2	chr8:61500400-61542200	Weak transcription	Hela-S3	cervix
3	chr8:61506000-61523200	Weak transcription	Fetal Heart	heart
4	chr8:61506000-61532200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr8:61506400-61532400	Weak transcription	NHLF	lung
6	chr8:61508000-61521600	Weak transcription	NHEK	skin
7	chr8:61508800-61533000	Weak transcription	HUVEC	blood vessel
8	chr8:61512400-61519600	Strong transcription	Osteobl	bone
9	chr8:61512400-61526200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr8:61512600-61518400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:61512600-61521800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr8:61512800-61518600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:61512800-61522600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr8:61512800-61527800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr8:61513000-61519600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr8:61513000-61528400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr8:61513800-61519400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr8:61514200-61519200	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr8:61514400-61518800	ZNF genes & repeats	GM12878-XiMat	blood
20	chr8:61514800-61519000	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr8:61515000-61519600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:61515200-61518400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr8:61515200-61519000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr8:61515200-61519400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr8:61515200-61519600	Strong transcription	Fetal Kidney	kidney
26	chr8:61515400-61518400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
27	chr8:61515400-61518400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr8:61515600-61521600	Weak transcription	Right Ventricle	heart
29	chr8:61515600-61532200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr8:61515600-61533400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr8:61516000-61518400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
32	chr8:61516000-61532000	Weak transcription	NHDF-Ad	bronchial
33	chr8:61516200-61521400	Weak transcription	HMEC	breast
34	chr8:61516200-61533200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr8:61516400-61518400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr8:61516400-61518400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
37	chr8:61516800-61518800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr8:61516800-61520400	Strong transcription	Liver	Liver
39	chr8:61517000-61518400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
40	chr8:61517000-61518800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
41	chr8:61517600-61519200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
42	chr8:61517600-61520000	Strong transcription	Adipose Nuclei	Adipose
43	chr8:61517600-61520400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr8:61517800-61518400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr8:61517800-61522200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr8:61517800-61532200	Weak transcription	Small Intestine	intestine
47	chr8:61517800-61537800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr8:61518000-61518400	Weak transcription	Primary B cells from cord blood	blood
49	chr8:61518000-61521400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr8:61518000-61521400	Weak transcription	HepG2	liver

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