Variant report

Variant	rs4910085
Chromosome Location	chr11:9981297-9981298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10160515	0.81[AMR][1000 genomes]
rs10770080	0.83[CHB][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs10770082	0.92[YRI][hapmap]
rs10770084	0.92[YRI][hapmap]
rs10840331	0.92[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10840332	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10840335	0.92[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10840339	0.88[AMR][1000 genomes]
rs10840346	0.80[ASW][hapmap];0.85[YRI][hapmap]
rs10840357	0.89[YRI][hapmap]
rs10840358	0.89[YRI][hapmap]
rs10840363	0.89[YRI][hapmap]
rs11042575	0.85[CEU][hapmap]
rs11042581	0.88[AMR][1000 genomes]
rs11042582	0.85[CEU][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes]
rs12288355	0.92[YRI][hapmap]
rs12295754	0.88[AMR][1000 genomes]
rs12360854	0.92[YRI][hapmap]
rs2403228	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2403230	0.80[ASW][hapmap];0.92[YRI][hapmap]
rs2403259	0.83[CHB][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes]
rs2403264	0.82[YRI][hapmap]
rs4309158	0.82[CEU][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes]
rs4910088	0.84[AMR][1000 genomes]
rs4910089	0.92[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs6483846	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6483860	0.95[AMR][1000 genomes]
rs6483883	0.80[ASW][hapmap];0.83[CHB][hapmap];0.87[MEX][hapmap];0.96[YRI][hapmap]
rs66922162	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7102016	0.80[ASW][hapmap];0.95[MEX][hapmap]
rs7119000	0.80[ASW][hapmap];0.89[YRI][hapmap]
rs7121704	0.80[ASW][hapmap];0.92[YRI][hapmap]
rs7126376	0.82[YRI][hapmap]
rs7128698	0.80[ASW][hapmap];0.91[MEX][hapmap];0.96[YRI][hapmap]
rs7129239	0.82[AMR][1000 genomes]
rs7932988	0.88[YRI][hapmap]
rs7933482	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7936351	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7950140	0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv1819684	chr11:9973062-10012511	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv982983	chr11:9980342-9981342	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4910085	OR52B2	cis	parietal	SCAN
rs4910085	SYT9	cis	cerebellum	SCAN
rs4910085	TRIM66	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9952800-9995200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:9968000-9984000	Weak transcription	Primary B cells from cord blood	blood
3	chr11:9968000-9984200	Weak transcription	Fetal Kidney	kidney
4	chr11:9973000-9986000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:9973800-10010600	Weak transcription	Fetal Brain Male	brain
6	chr11:9974200-9994400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr11:9974200-9994600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:9974200-9994800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr11:9974200-9999000	Weak transcription	Fetal Heart	heart
10	chr11:9974200-9999000	Weak transcription	HSMMtube	muscle
11	chr11:9974400-9982800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:9975400-9985600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:9977000-9994400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr11:9977600-9982000	Weak transcription	Stomach Mucosa	stomach
15	chr11:9977800-9981600	Strong transcription	Fetal Lung	lung
16	chr11:9978200-9981600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:9978600-9981800	Strong transcription	Left Ventricle	heart
18	chr11:9978600-9986000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:9978800-9985000	Weak transcription	Small Intestine	intestine
20	chr11:9979400-9981600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr11:9979400-9982000	Weak transcription	Colonic Mucosa	Colon
22	chr11:9979400-9986000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:9979400-9995000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr11:9979600-9981600	Strong transcription	Fetal Muscle Leg	muscle
25	chr11:9979600-9981800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:9979600-9982000	Strong transcription	Fetal Stomach	stomach
27	chr11:9979600-9985600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:9979600-9985800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:9979600-9994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:9979800-9987400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr11:9979800-9999200	Weak transcription	NH-A	brain
32	chr11:9980000-9981600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:9980000-9982200	Weak transcription	Thymus	Thymus
34	chr11:9980200-9981400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:9980200-9981400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:9980200-9981400	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr11:9980200-9981400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr11:9980200-9981400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:9980200-9981400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:9980200-9981400	Strong transcription	Aorta	Aorta
41	chr11:9980200-9981400	Strong transcription	Colon Smooth Muscle	Colon
42	chr11:9980200-9981400	Strong transcription	Fetal Intestine Large	intestine
43	chr11:9980200-9981400	Strong transcription	Fetal Intestine Small	intestine
44	chr11:9980200-9981400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr11:9980200-9981400	Strong transcription	Rectal Smooth Muscle	rectum
46	chr11:9980200-9981400	Strong transcription	Right Ventricle	heart
47	chr11:9980200-9981400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr11:9980200-9981400	Strong transcription	NHLF	lung
49	chr11:9980200-9981800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:9980200-9981800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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