Variant report

Variant	rs3824867
Chromosome Location	chr11:47468569-47468570
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	chr11:47466850..47468725-chr11:47468990..47470844,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165917	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1044269	0.92[GIH][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs10742805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10742806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10742816	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs10769267	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11819955	0.93[JPT][hapmap]
rs11820650	0.82[ASN][1000 genomes]
rs11820680	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11821917	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11824864	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11828339	0.88[GIH][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12282783	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12419342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474056	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs17198158	0.88[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs17790804	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2138767	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs2242511	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs3740684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3740685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781628	0.81[ASN][1000 genomes]
rs3847503	0.88[GIH][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4147730	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs4237544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4282946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752783	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs4752786	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs4752829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752836	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752839	0.81[GIH][hapmap];0.89[JPT][hapmap]
rs4752843	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs4752992	0.81[ASN][1000 genomes]
rs60380053	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60882887	0.83[ASN][1000 genomes]
rs61000762	0.83[ASN][1000 genomes]
rs7101772	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7104366	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7105122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107853	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7108143	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7111873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7117277	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7119556	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7125468	0.83[ASN][1000 genomes]
rs7126210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7130693	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs753812	0.88[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7931089	0.92[JPT][hapmap]
rs7948705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9666924	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs9734013	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9919526	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv975328	chr11:47446815-47471052	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3824867	FAM92A3	trans	cerebellum	SCAN
rs3824867	MDK	cis	parietal	SCAN
rs3824867	PTPRJ	cis	parietal	SCAN
rs3824867	PSMC3	cis	cerebellum	SCAN
rs3824867	ACP2	cis	brain	BrainEAC
rs3824867	MADD	cis	parietal	SCAN
rs3824867	PACSIN3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:47453400-47469200	Weak transcription	Psoas Muscle	Psoas
3	chr11:47453400-47480000	Weak transcription	Thymus	Thymus
4	chr11:47456600-47468600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr11:47457400-47480200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:47457400-47480800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:47457400-47488400	Weak transcription	Gastric	stomach
8	chr11:47457800-47469000	Weak transcription	Spleen	Spleen
9	chr11:47459800-47469400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:47459800-47470800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:47459800-47480600	Weak transcription	Fetal Intestine Small	intestine
12	chr11:47459800-47480800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:47460000-47470800	Weak transcription	Lung	lung
14	chr11:47460000-47475600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:47460600-47469200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:47461800-47480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:47463600-47469200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:47463600-47469200	Weak transcription	Placenta	Placenta
19	chr11:47463600-47469400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:47464000-47481000	Weak transcription	NHEK	skin
21	chr11:47464800-47468600	Weak transcription	HSMMtube	muscle
22	chr11:47465000-47480800	Weak transcription	Adipose Nuclei	Adipose
23	chr11:47465200-47469000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:47465200-47475600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:47465400-47468600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr11:47465400-47470400	Weak transcription	Left Ventricle	heart
27	chr11:47465800-47480800	Weak transcription	Primary T cells from cord blood	blood
28	chr11:47466000-47471200	Weak transcription	Liver	Liver
29	chr11:47466000-47475600	Weak transcription	Fetal Thymus	thymus
30	chr11:47466200-47469000	Weak transcription	HepG2	liver
31	chr11:47467600-47469000	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr11:47467800-47468800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr11:47467800-47475600	Weak transcription	Colon Smooth Muscle	Colon
34	chr11:47468000-47468800	Enhancers	HUVEC	blood vessel
35	chr11:47468200-47469000	Genic enhancers	Fetal Muscle Leg	muscle
36	chr11:47468400-47469600	Transcr. at gene 5' and 3'	HSMM	muscle

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