Variant report

Variant	rs3753051
Chromosome Location	chr11:76257215-76257216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10160382	0.80[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs10793169	0.84[CEU][hapmap]
rs10793171	0.84[CEU][hapmap]
rs10899227	0.81[CEU][hapmap]
rs17245270	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17450692	0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17749618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939467	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1939468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282611	0.91[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2508740	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs2508741	0.80[CEU][hapmap];0.80[GIH][hapmap]
rs2508760	0.81[CEU][hapmap]
rs2508761	0.81[CEU][hapmap]
rs2508762	0.80[CEU][hapmap]
rs2513504	0.85[CEU][hapmap]
rs2513508	0.81[CEU][hapmap]
rs2513513	0.85[CEU][hapmap]
rs2513520	0.81[CEU][hapmap]
rs2513525	0.85[CEU][hapmap]
rs3814711	0.84[CEU][hapmap]
rs4245443	0.81[CEU][hapmap]
rs4272809	0.81[CEU][hapmap]
rs4300410	0.81[CEU][hapmap]
rs4945090	0.81[CEU][hapmap]
rs55904328	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55975198	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159348	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56294280	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56393414	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56394729	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58015965	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59168723	0.93[ASN][1000 genomes]
rs61894507	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61894512	0.85[AFR][1000 genomes]
rs61894542	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61894543	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61894546	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7107058	0.80[CEU][hapmap]
rs7107442	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7115331	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs7116583	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7123361	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7125552	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72930511	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7926009	0.81[CEU][hapmap]
rs7927515	0.80[CEU][hapmap]
rs7928373	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7936656	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7938856	0.81[CHD][hapmap];0.92[MEX][hapmap]
rs7941790	0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs7942257	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7949258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7951867	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8848	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050713	chr11:76147085-76267117	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1848387	chr11:76243699-76262652	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3753051	SLCO2B1	cis	cerebellum	SCAN
rs3753051	ARHGEF17	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76224400-76262600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr11:76224400-76263800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:76230000-76265600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:76233600-76258800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr11:76233800-76258600	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr11:76233800-76260200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:76233800-76262000	Strong transcription	Placenta	Placenta
8	chr11:76233800-76262400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:76233800-76262600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr11:76233800-76263200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:76234000-76262600	Strong transcription	Dnd41	blood
12	chr11:76234200-76262000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:76234800-76263000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr11:76236400-76261800	Weak transcription	Stomach Mucosa	stomach
15	chr11:76237400-76261200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:76239000-76259800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr11:76239000-76261600	Strong transcription	Liver	Liver
18	chr11:76239600-76259000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:76239600-76262000	Strong transcription	Primary T cells from cord blood	blood
20	chr11:76239600-76262200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr11:76239800-76259400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:76246000-76257600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr11:76246200-76257400	Strong transcription	Fetal Muscle Leg	muscle
24	chr11:76246400-76257600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:76246600-76260600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:76248200-76261400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:76248400-76259600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:76248400-76261600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:76248600-76257400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:76250200-76258000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:76250200-76259200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:76250600-76257400	Strong transcription	GM12878-XiMat	blood
33	chr11:76251600-76260400	Strong transcription	Fetal Lung	lung
34	chr11:76252000-76257800	Strong transcription	Primary hematopoietic stem cells	blood
35	chr11:76252000-76257800	Strong transcription	Fetal Intestine Large	intestine
36	chr11:76252000-76257800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr11:76252000-76258000	Strong transcription	Brain Substantia Nigra	brain
38	chr11:76252000-76259200	Strong transcription	Primary B cells from cord blood	blood
39	chr11:76252000-76262000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr11:76252000-76262600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:76252200-76260600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:76252600-76257400	Strong transcription	Brain Cingulate Gyrus	brain
43	chr11:76252600-76257400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr11:76252600-76258200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr11:76252600-76258200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:76252600-76258200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr11:76252600-76259200	Strong transcription	Fetal Thymus	thymus
48	chr11:76252600-76261800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr11:76252600-76263000	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr11:76252800-76257400	Strong transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links