Variant report

Variant	rs2502750
Chromosome Location	chr9:136689495-136689496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136675111..136676844-chr9:136688260..136691253,2	K562	blood:
2	chr9:136687210..136690877-chr9:136692524..136697595,4	MCF-7	breast:
3	chr9:136688132..136689983-chr9:136690497..136693313,2	MCF-7	breast:
4	chr9:136677495..136679491-chr9:136688061..136690031,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10123394	1.00[CHB][hapmap]
rs10993810	0.80[EUR][1000 genomes]
rs10993811	0.80[EUR][1000 genomes]
rs10993812	0.82[EUR][1000 genomes]
rs10993815	0.82[EUR][1000 genomes]
rs1179486	1.00[CHB][hapmap]
rs12337948	0.82[EUR][1000 genomes]
rs12338059	0.80[EUR][1000 genomes]
rs17663527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs2428092	1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs2428095	0.91[YRI][hapmap]
rs2486335	0.81[AFR][1000 genomes]
rs2486337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs2486338	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2486339	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2486341	0.83[YRI][hapmap]
rs2488551	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs2488556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2488557	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2502749	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2502751	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502752	0.89[EUR][1000 genomes]
rs28435685	0.82[EUR][1000 genomes]
rs28493540	0.89[EUR][1000 genomes]
rs28647613	0.82[EUR][1000 genomes]
rs3858100	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs3858101	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs3858102	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858103	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs4059239	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55776501	0.90[EUR][1000 genomes]
rs62576521	0.82[EUR][1000 genomes]
rs62576522	0.82[EUR][1000 genomes]
rs62576523	0.82[EUR][1000 genomes]
rs7029322	0.88[EUR][1000 genomes]
rs7034680	0.84[EUR][1000 genomes]
rs7037626	0.80[EUR][1000 genomes]
rs7038003	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs7042529	0.89[EUR][1000 genomes]
rs7046253	0.80[EUR][1000 genomes]
rs7848976	1.00[CHB][hapmap]
rs9409864	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894114	chr9:136538798-136779153	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv428546	chr9:136541745-136720872	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv831745	chr9:136593702-136780273	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv894117	chr9:136600201-136716399	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv831746	chr9:136607829-136750740	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv894121	chr9:136629399-136692787	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv894122	chr9:136632662-136760639	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1035272	chr9:136665308-136772256	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2502750	VAV2	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136643200-136689800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:136657800-136690600	Weak transcription	Fetal Kidney	kidney
3	chr9:136658600-136691400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr9:136658800-136705400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:136659000-136702200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:136661400-136693800	Weak transcription	HMEC	breast
7	chr9:136667800-136690600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:136669000-136691200	Weak transcription	NH-A	brain
9	chr9:136669800-136689800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:136670000-136692600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:136673200-136705000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:136674600-136699000	Weak transcription	Aorta	Aorta
13	chr9:136675200-136728400	Weak transcription	Esophagus	oesophagus
14	chr9:136675400-136691600	Weak transcription	Lung	lung
15	chr9:136675400-136703200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:136675400-136709400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:136675600-136698000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:136675600-136704800	Weak transcription	Adipose Nuclei	Adipose
19	chr9:136676000-136699800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:136677000-136705000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:136679200-136696800	Weak transcription	Gastric	stomach
22	chr9:136679800-136691600	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:136680000-136696800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:136680200-136691200	Weak transcription	Fetal Brain Female	brain
25	chr9:136680200-136691400	Weak transcription	Right Ventricle	heart
26	chr9:136680200-136691800	Weak transcription	Right Atrium	heart
27	chr9:136680200-136693600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:136680200-136693800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:136680400-136690400	Weak transcription	Brain Germinal Matrix	brain
30	chr9:136681400-136690800	Weak transcription	Fetal Lung	lung
31	chr9:136682200-136692400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:136682200-136701000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:136683800-136691000	Weak transcription	HSMM	muscle
34	chr9:136683800-136705000	Weak transcription	NHDF-Ad	bronchial
35	chr9:136684000-136694400	Weak transcription	Hela-S3	cervix
36	chr9:136684200-136690800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:136684200-136691200	Strong transcription	Fetal Intestine Small	intestine
38	chr9:136684200-136696800	Weak transcription	Osteobl	bone
39	chr9:136684200-136704800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr9:136684600-136690400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:136684600-136691600	Weak transcription	Brain Substantia Nigra	brain
42	chr9:136685400-136690000	Enhancers	Primary B cells from cord blood	blood
43	chr9:136686000-136690600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:136686000-136690600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr9:136686000-136709600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr9:136686200-136692200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:136686400-136690000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:136686600-136690800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:136686600-136690800	Weak transcription	NHLF	lung
50	chr9:136686600-136692200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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