Variant report

Variant	rs3824854
Chromosome Location	chr11:63885305-63885306
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	chr11:63751447..63755451-chr11:63882751..63885607,3	MCF-7	breast:
2	chr11:63884385..63886576-chr11:63893083..63896548,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167770	Chromatin interaction
ENSG00000133315	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1058735	0.86[CEU][hapmap];0.87[CHB][hapmap];0.84[EUR][1000 genomes]
rs1059440	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11231701	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11601024	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11601577	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11602181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603042	0.81[CHB][hapmap]
rs11603212	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11605738	0.86[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs11606544	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607007	0.86[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11607144	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11607165	0.93[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12418035	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12574258	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12575642	0.86[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12787852	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12794145	0.86[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs12797120	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12798333	0.87[CHD][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs12802950	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2001003	0.86[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs2015226	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2070765	0.86[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2154986	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2282490	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2875749	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34089806	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34113693	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34838337	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35090903	0.84[EUR][1000 genomes]
rs35095324	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35458188	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35524387	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35858916	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3802933	0.93[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58632573	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591837	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66648159	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67546972	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs677447	0.83[YRI][hapmap]
rs7102327	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7112277	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7130030	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71479474	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72918475	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72920332	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7939784	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7944061	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7952318	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs882146	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
3	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
4	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv832184	chr11:63787702-63925084	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
7	nsv897658	chr11:63810944-63897759	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv897659	chr11:63813470-63907079	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
10	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
11	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
12	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
13	nsv356	chr11:63868847-63913129	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3824854	PRDX5	cis	parietal	SCAN
rs3824854	PPP1R14B	Cis_1M	lymphoblastoid	RTeQTL
rs3824854	GPHA2	cis	cerebellum	SCAN
rs3824854	FAU	cis	parietal	SCAN
rs3824854	ASRGL1	cis	parietal	SCAN
rs3824854	PPP1R14B	cis	Heart Left Ventricle	GTEx
rs3824854	PPP1R14B	cis	lymphoblastoid	seeQTL
rs3824854	FKBP2	cis	parietal	SCAN
rs3824854	FAM89B	cis	parietal	SCAN
rs3824854	TRPT1	cis	Muscle Skeletal	GTEx
rs3824854	PPP1R14B	cis	multi-tissue	Pritchard
rs3824854	CD248	cis	parietal	SCAN
rs3824854	SLC22A10	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63866400-63887800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:63873400-63886800	Weak transcription	Colonic Mucosa	Colon
3	chr11:63875400-63896200	Weak transcription	Spleen	Spleen
4	chr11:63875600-63886800	Weak transcription	HSMMtube	muscle
5	chr11:63879200-63888400	Weak transcription	Left Ventricle	heart
6	chr11:63879600-63885800	Weak transcription	HepG2	liver
7	chr11:63879600-63886200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:63879600-63890200	Weak transcription	Liver	Liver
9	chr11:63879800-63891600	Weak transcription	Primary T cells from cord blood	blood
10	chr11:63881200-63888000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:63881800-63891800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:63882200-63889400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:63882200-63889600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:63882200-63889600	Weak transcription	Lung	lung
15	chr11:63882200-63892800	Weak transcription	Fetal Kidney	kidney
16	chr11:63882800-63888000	Strong transcription	Fetal Stomach	stomach
17	chr11:63883000-63890800	Weak transcription	Dnd41	blood
18	chr11:63883200-63888400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:63883400-63885400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr11:63883400-63885800	Strong transcription	Brain Hippocampus Middle	brain
21	chr11:63883400-63886400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:63883600-63885800	Strong transcription	Fetal Muscle Leg	muscle
23	chr11:63883600-63886200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:63883600-63888200	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:63883600-63888200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:63883800-63885400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:63883800-63885600	Strong transcription	Brain Substantia Nigra	brain
28	chr11:63883800-63885600	Genic enhancers	Fetal Brain Female	brain
29	chr11:63883800-63886000	Strong transcription	Brain Germinal Matrix	brain
30	chr11:63883800-63886000	Weak transcription	Fetal Brain Male	brain
31	chr11:63883800-63886600	Strong transcription	Brain Cingulate Gyrus	brain
32	chr11:63883800-63888400	Weak transcription	Fetal Heart	heart
33	chr11:63884200-63885400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:63884200-63885400	Strong transcription	Fetal Intestine Small	intestine
35	chr11:63884200-63885600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:63884200-63885600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:63884200-63885600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:63884200-63885800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:63884400-63885600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:63884400-63885600	Strong transcription	Gastric	stomach
41	chr11:63884400-63885800	Genic enhancers	Right Ventricle	heart
42	chr11:63884600-63885800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:63884600-63887200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr11:63884600-63889800	Weak transcription	Pancreas	Pancrea
45	chr11:63884800-63885800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:63884800-63888400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:63885000-63885400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:63885000-63887400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:63885000-63896600	Weak transcription	Hela-S3	cervix
50	chr11:63885200-63885400	Genic enhancers	Brain Angular Gyrus	brain

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