Variant report

Variant	rs3741021
Chromosome Location	chr11:33692315-33692316
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:33689243..33690846-chr11:33691492..33694193,2	MCF-7	breast:
2	chr11:33689412..33692337-chr11:33694511..33696205,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10742302	0.81[CEU][hapmap]
rs10836085	0.81[CEU][hapmap]
rs10836094	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10836095	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10836097	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1096557	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11032332	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11032335	0.84[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11032338	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11601472	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12226271	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12280103	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12574994	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321015	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1321016	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2295064	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3741020	0.86[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781839	0.93[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101438	0.93[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831622	0.92[AMR][1000 genomes];0.85[EUR][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	nsv832113	chr11:33609202-33767781	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3741021	PRRG4	cis	cerebellum	SCAN
rs3741021	C11orf41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33674800-33700000	Weak transcription	Brain Angular Gyrus	brain
2	chr11:33678800-33695400	Weak transcription	Brain Anterior Caudate	brain
3	chr11:33685200-33697800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:33689400-33692800	Enhancers	Stomach Mucosa	stomach
5	chr11:33689400-33693000	Enhancers	NHEK	skin
6	chr11:33689400-33693800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:33689800-33693400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:33689800-33695600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:33690000-33695600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr11:33690400-33693600	Weak transcription	Fetal Brain Female	brain
11	chr11:33690600-33693000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:33690600-33693200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:33690800-33693000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:33690800-33694400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:33691000-33693000	Enhancers	NHDF-Ad	bronchial
16	chr11:33691000-33693800	Enhancers	NHLF	lung
17	chr11:33691000-33694000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:33691000-33694000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:33691000-33695600	Weak transcription	Fetal Muscle Leg	muscle
20	chr11:33691000-33695600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr11:33691000-33701600	Weak transcription	Gastric	stomach
22	chr11:33691000-33712400	Weak transcription	Psoas Muscle	Psoas
23	chr11:33691200-33692400	Weak transcription	Esophagus	oesophagus
24	chr11:33691200-33692600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:33691200-33692600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:33691200-33692800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:33691200-33693000	Enhancers	NH-A	brain
28	chr11:33691400-33692400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:33691400-33692600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr11:33691400-33692800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:33691400-33693000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:33691400-33693000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:33691400-33693000	Enhancers	HUVEC	blood vessel
34	chr11:33691400-33693200	Enhancers	Osteobl	bone
35	chr11:33691400-33696800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:33691600-33692600	Enhancers	HSMMtube	muscle
37	chr11:33691600-33693000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr11:33691600-33693000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:33691600-33693000	Enhancers	HSMM	muscle
40	chr11:33691600-33693200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:33691600-33693200	Enhancers	HMEC	breast
42	chr11:33691800-33704200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr11:33692000-33692600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:33692000-33693200	Enhancers	GM12878-XiMat	blood
45	chr11:33692200-33693000	Strong transcription	Brain Germinal Matrix	brain
46	chr11:33692200-33693200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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