Variant report

Variant	rs12541086
Chromosome Location	chr8:48236907-48236908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1038797	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10808752	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10957074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11774001	0.92[EUR][1000 genomes]
rs11775514	0.86[EUR][1000 genomes]
rs11775628	0.87[EUR][1000 genomes]
rs11779308	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs11779423	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs11781727	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11783141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11784823	0.82[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs11785228	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12543823	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12547513	0.91[EUR][1000 genomes]
rs12680669	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12682269	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13259872	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs13259913	0.90[EUR][1000 genomes]
rs16925242	0.92[YRI][hapmap]
rs2087656	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs2130879	0.86[EUR][1000 genomes]
rs2172121	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs2362554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34099416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35045730	0.90[EUR][1000 genomes]
rs4242439	0.92[CEU][hapmap]
rs4388466	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap]
rs4498545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4536257	0.92[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.97[MKK][hapmap]
rs4872957	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs4873102	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs4873106	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4873293	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4873368	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs6472229	0.93[EUR][1000 genomes]
rs6981790	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6982620	0.82[CHD][hapmap]
rs6990123	0.95[EUR][1000 genomes]
rs6994218	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7012341	0.91[EUR][1000 genomes]
rs7819806	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs7826284	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7839134	0.91[EUR][1000 genomes]
rs876915	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs902619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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	nsv1028036	chr8:47531749-48256108	Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv1019289	chr8:47536056-48251883	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv539591	chr8:47536056-48251883	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1015347	chr8:47698082-48318579	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv539593	chr8:47698082-48318579	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1031331	chr8:48163412-48239160	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1032993	chr8:48167423-48246277	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1030486	chr8:48167423-48247297	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv2758155	chr8:48188989-48321308	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv2759610	chr8:48188989-48321308	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv1817304	chr8:48205314-48321308	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12541086	MCM4	cis	cerebellum	SCAN
rs12541086	KIAA0146	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48207400-48238200	Weak transcription	Aorta	Aorta
2	chr8:48207400-48258000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr8:48207600-48245600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr8:48207600-48248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:48208400-48240000	Weak transcription	Placenta	Placenta
6	chr8:48208400-48243800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr8:48208800-48242400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr8:48209400-48266000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr8:48210000-48242800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr8:48210600-48243000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr8:48216200-48249600	Weak transcription	Ovary	ovary
12	chr8:48216200-48252400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr8:48216800-48242600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr8:48222000-48243000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:48222400-48242800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr8:48222600-48242600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr8:48222600-48242800	Weak transcription	Primary T cells from cord blood	blood
18	chr8:48222600-48243000	Weak transcription	HSMM	muscle
19	chr8:48222800-48243200	Weak transcription	Fetal Muscle Leg	muscle
20	chr8:48223400-48242800	Weak transcription	Fetal Intestine Large	intestine
21	chr8:48223400-48252600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr8:48223600-48242000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr8:48223800-48242800	Weak transcription	GM12878-XiMat	blood
24	chr8:48224400-48237200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr8:48224400-48237400	Weak transcription	Esophagus	oesophagus
26	chr8:48224400-48240800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr8:48224400-48243000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr8:48228000-48243200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr8:48228000-48243400	Weak transcription	Liver	Liver
30	chr8:48228200-48242800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr8:48228200-48243400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr8:48228200-48243400	Weak transcription	Fetal Kidney	kidney
33	chr8:48228200-48246200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr8:48228200-48248800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr8:48228200-48251200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:48228200-48254400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr8:48228200-48256000	Weak transcription	Left Ventricle	heart
38	chr8:48228600-48242800	Weak transcription	Fetal Lung	lung
39	chr8:48228600-48265800	Weak transcription	K562	blood
40	chr8:48229800-48237400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr8:48230000-48252400	Weak transcription	Lung	lung
42	chr8:48230200-48242000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr8:48230200-48248200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr8:48230400-48240000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr8:48230400-48242800	Weak transcription	Primary B cells from cord blood	blood
46	chr8:48230400-48248200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr8:48230400-48252200	Weak transcription	Fetal Stomach	stomach
48	chr8:48230400-48256200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr8:48230400-48267400	Weak transcription	Spleen	Spleen
50	chr8:48230600-48242400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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