Variant report

Variant	rs9548882
Chromosome Location	chr13:40263979-40263980
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	chr13:40263482..40266386-chr13:40274565..40277174,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12584772	0.88[GIH][hapmap];0.92[TSI][hapmap]
rs4329796	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4346098	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4570710	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4603426	0.83[AMR][1000 genomes]
rs7329513	0.88[GIH][hapmap];0.92[TSI][hapmap]
rs7988187	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7989518	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7994943	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs9315726	0.96[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9532423	1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs9532427	0.88[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap]
rs9548849	0.92[EUR][1000 genomes]
rs9548874	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9548886	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9548887	0.88[CEU][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9548889	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9548890	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9548892	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9548925	0.83[AMR][1000 genomes]
rs9566464	1.00[CEU][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9566468	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9576878	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs9576879	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9576883	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9576885	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9576886	0.86[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9576888	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv870429	chr13:40235061-40265634	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv471130	chr13:40261945-40350912	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548882	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs9548882	COG6	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
2	chr13:40231000-40266200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr13:40231400-40264200	Weak transcription	Esophagus	oesophagus
6	chr13:40231400-40268000	Weak transcription	Small Intestine	intestine
7	chr13:40231600-40270200	Weak transcription	Gastric	stomach
8	chr13:40233000-40273600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
10	chr13:40238000-40291600	Weak transcription	Fetal Intestine Small	intestine
11	chr13:40246400-40297400	Weak transcription	HUVEC	blood vessel
12	chr13:40253000-40266200	Weak transcription	Colon Smooth Muscle	Colon
13	chr13:40253400-40266600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr13:40254600-40264000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr13:40255000-40264200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:40255000-40266600	Weak transcription	Fetal Stomach	stomach
17	chr13:40255000-40268000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:40255000-40270000	Weak transcription	Lung	lung
19	chr13:40255000-40291200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr13:40255200-40265800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr13:40255200-40272800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:40255200-40291000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:40255400-40266800	Weak transcription	NHLF	lung
25	chr13:40255400-40272800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr13:40255600-40264200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr13:40255600-40266800	Weak transcription	Brain Angular Gyrus	brain
28	chr13:40255600-40270800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr13:40255600-40272800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr13:40255600-40283600	Weak transcription	Fetal Brain Male	brain
31	chr13:40255800-40266600	Weak transcription	Brain Hippocampus Middle	brain
32	chr13:40255800-40271000	Weak transcription	Ovary	ovary
33	chr13:40255800-40283800	Weak transcription	Brain Anterior Caudate	brain
34	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
35	chr13:40256800-40264800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr13:40257600-40264200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:40257600-40264600	Weak transcription	Fetal Thymus	thymus
38	chr13:40257600-40274600	Weak transcription	HMEC	breast
39	chr13:40257600-40310800	Weak transcription	Brain Germinal Matrix	brain
40	chr13:40257800-40269200	Weak transcription	Fetal Kidney	kidney
41	chr13:40257800-40273200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr13:40258200-40266600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr13:40258200-40289800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr13:40261000-40265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr13:40261400-40264600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr13:40261400-40264600	Strong transcription	Placenta	Placenta
47	chr13:40261600-40264600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr13:40261800-40264000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr13:40261800-40264600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:40262000-40271200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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