Variant report

Variant	rs12548874
Chromosome Location	chr8:95935164-95935165
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	chr8:95932664..95935352-chr8:95936830..95938915,3	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10086284	0.86[CHB][hapmap]
rs10098778	0.86[CHB][hapmap];0.86[GIH][hapmap]
rs10099941	0.86[CHB][hapmap]
rs10100651	0.84[ASN][1000 genomes]
rs10104909	0.86[CHB][hapmap]
rs10108430	0.83[EUR][1000 genomes]
rs10112232	0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap]
rs10441538	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs10956930	0.86[CHB][hapmap]
rs10956931	0.86[CHB][hapmap]
rs10956932	0.86[CHB][hapmap]
rs10956934	0.81[EUR][1000 genomes]
rs1129152	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.85[ASN][1000 genomes]
rs11996455	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs12155666	0.81[EUR][1000 genomes]
rs12546365	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12548999	0.86[CHB][hapmap]
rs12549003	0.86[CHB][hapmap]
rs12550765	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs1320164	0.81[EUR][1000 genomes]
rs13254283	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13255935	0.81[EUR][1000 genomes]
rs13257021	0.82[CEU][hapmap]
rs13262110	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13271375	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs13271644	0.93[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap]
rs1453377	0.86[CHB][hapmap];0.84[GIH][hapmap]
rs1453379	0.86[CHB][hapmap]
rs16893776	0.86[CHB][hapmap];0.86[GIH][hapmap]
rs2123647	0.86[CHB][hapmap]
rs2340584	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2945554	0.86[CHB][hapmap]
rs3802193	0.86[CHB][hapmap]
rs4075835	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4500055	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs4735331	0.86[CHB][hapmap]
rs4735332	0.86[CHB][hapmap]
rs4735333	0.85[EUR][1000 genomes]
rs4735336	0.86[CHB][hapmap];0.86[GIH][hapmap]
rs4735337	0.86[CHB][hapmap];0.86[GIH][hapmap]
rs4735339	0.86[CHB][hapmap];0.86[GIH][hapmap]
rs61663478	0.83[EUR][1000 genomes]
rs6471497	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs6471503	0.86[CHB][hapmap]
rs6471504	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6982393	0.86[CHB][hapmap];0.86[GIH][hapmap]
rs6987752	0.81[EUR][1000 genomes]
rs6991067	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7001535	0.86[CHB][hapmap]
rs7002058	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7003387	0.82[EUR][1000 genomes]
rs7004862	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7015841	0.86[CHB][hapmap]
rs7017487	0.86[CHB][hapmap]
rs713113	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs7820818	0.86[CHB][hapmap]
rs7827478	0.86[CHB][hapmap]
rs7845219	0.89[CEU][hapmap];0.86[CHB][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs896852	0.82[EUR][1000 genomes]
rs896854	0.88[GIH][hapmap];0.85[TSI][hapmap]
rs896855	0.84[EUR][1000 genomes]
rs9650133	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv891203	chr8:95883232-95948202	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv891204	chr8:95883232-95965135	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12548874	TP53INP1	cis	parietal	SCAN
rs12548874	OR5A1	trans	cerebellum	SCAN
rs12548874	RBM12B	cis	cerebellum	SCAN
rs12548874	TP53INP1	cis	multi-tissue	Pritchard
rs12548874	LAPTM4B	cis	parietal	SCAN
rs12548874	RAD54B	cis	cerebellum	SCAN
rs12548874	TP53INP1	Cis_1M	lymphoblastoid	RTeQTL
rs12548874	INTS8	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95909400-95939000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr8:95909400-95941000	Weak transcription	Ovary	ovary
3	chr8:95909400-95941200	Weak transcription	Fetal Stomach	stomach
4	chr8:95909600-95937000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:95909600-95938400	Weak transcription	Primary T cells from cord blood	blood
6	chr8:95909600-95941800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr8:95909800-95940600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr8:95910000-95940200	Weak transcription	Thymus	Thymus
9	chr8:95910800-95940200	Weak transcription	Hela-S3	cervix
10	chr8:95918000-95940200	Weak transcription	Brain Anterior Caudate	brain
11	chr8:95918600-95947400	Weak transcription	Small Intestine	intestine
12	chr8:95918800-95935200	Weak transcription	Primary B cells from cord blood	blood
13	chr8:95919000-95941200	Weak transcription	Left Ventricle	heart
14	chr8:95919200-95935200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr8:95919200-95948600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:95920200-95938400	Weak transcription	NHDF-Ad	bronchial
17	chr8:95920400-95938000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr8:95921200-95936600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr8:95926200-95939600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr8:95926200-95946400	Weak transcription	Stomach Mucosa	stomach
21	chr8:95926400-95941200	Weak transcription	Pancreas	Pancrea
22	chr8:95927000-95940400	Weak transcription	Lung	lung
23	chr8:95928400-95936800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr8:95928600-95935200	Weak transcription	Liver	Liver
25	chr8:95928600-95938600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr8:95928600-95939000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr8:95928600-95939600	Weak transcription	Fetal Intestine Large	intestine
28	chr8:95928600-95939600	Weak transcription	Dnd41	blood
29	chr8:95928600-95940200	Weak transcription	Fetal Kidney	kidney
30	chr8:95928600-95940200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr8:95928600-95941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:95928600-95941200	Weak transcription	Fetal Intestine Small	intestine
33	chr8:95928800-95937200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr8:95928800-95939800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr8:95929800-95940600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr8:95930200-95941800	Weak transcription	Spleen	Spleen
37	chr8:95930600-95935400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr8:95930600-95936800	Weak transcription	Fetal Muscle Leg	muscle
39	chr8:95930600-95937400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr8:95930600-95938400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr8:95930600-95939800	Weak transcription	Fetal Lung	lung
42	chr8:95930600-95940800	Weak transcription	Aorta	Aorta
43	chr8:95930600-95948600	Weak transcription	Gastric	stomach
44	chr8:95930800-95937400	Weak transcription	Adipose Nuclei	Adipose
45	chr8:95931000-95937400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr8:95931200-95936800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr8:95931800-95950000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr8:95932000-95940400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr8:95932200-95936800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr8:95932200-95937200	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links