Variant report

Variant	rs12877931
Chromosome Location	chr13:50276679-50276680
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	chr13:50265034..50267165-chr13:50275444..50277736,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123179	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11148160	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11148167	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12430539	0.91[AFR][1000 genomes]
rs12584401	0.91[AFR][1000 genomes]
rs12864534	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12866447	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12868235	0.91[AFR][1000 genomes]
rs12869900	0.84[EUR][1000 genomes]
rs12875005	0.92[EUR][1000 genomes]
rs12876223	0.82[EUR][1000 genomes]
rs12876889	0.92[EUR][1000 genomes]
rs1535543	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1575387	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1923730	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2025264	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2146143	0.91[ASN][1000 genomes]
rs2236354	0.91[AFR][1000 genomes]
rs34423763	0.92[EUR][1000 genomes]
rs35331571	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742095	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4603448	0.91[AFR][1000 genomes]
rs4643206	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4941657	0.91[AFR][1000 genomes]
rs4942864	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4942870	0.91[AFR][1000 genomes]
rs6561550	0.91[ASN][1000 genomes]
rs6561552	0.91[ASN][1000 genomes]
rs6561553	0.87[ASN][1000 genomes]
rs73192666	0.91[ASN][1000 genomes]
rs7446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997798	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942032	0.91[ASN][1000 genomes]
rs9526592	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526595	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9535287	0.82[ASN][1000 genomes]
rs9535301	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9535302	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535309	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535315	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535326	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9535333	0.86[EUR][1000 genomes]
rs9535339	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9535344	0.81[AFR][1000 genomes]
rs9535345	0.81[AFR][1000 genomes]
rs9535347	0.91[AFR][1000 genomes]
rs9535352	0.91[AFR][1000 genomes]
rs9535356	0.91[AFR][1000 genomes]
rs9568309	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12877931	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs12877931	EBPL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266000-50278200	Weak transcription	Lung	lung
2	chr13:50266000-50284200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:50266200-50279200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:50266200-50279400	Weak transcription	Brain Angular Gyrus	brain
5	chr13:50266200-50279400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:50266200-50282200	Weak transcription	Brain Germinal Matrix	brain
7	chr13:50266200-50285600	Weak transcription	NHLF	lung
8	chr13:50266200-50286000	Weak transcription	Psoas Muscle	Psoas
9	chr13:50266200-50289400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr13:50266200-50289600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr13:50266200-50295200	Weak transcription	Spleen	Spleen
12	chr13:50266200-50296000	Weak transcription	K562	blood
13	chr13:50266200-50298600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:50266200-50298800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr13:50266200-50307800	Weak transcription	Gastric	stomach
16	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr13:50266400-50281400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr13:50266400-50289400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr13:50266400-50293600	Weak transcription	Colonic Mucosa	Colon
20	chr13:50266400-50295800	Weak transcription	Small Intestine	intestine
21	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
22	chr13:50266600-50279000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr13:50266800-50279000	Weak transcription	NHEK	skin
24	chr13:50266800-50279400	Weak transcription	Colon Smooth Muscle	Colon
25	chr13:50267200-50289400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr13:50270400-50286400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:50270800-50277200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:50271400-50276800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:50271400-50284800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr13:50271400-50286400	Strong transcription	Dnd41	blood
31	chr13:50271400-50286800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:50271600-50284400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:50271800-50277000	Strong transcription	HSMM	muscle
34	chr13:50272400-50295000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:50272400-50296000	Weak transcription	Fetal Heart	heart
36	chr13:50273000-50277200	Strong transcription	Liver	Liver
37	chr13:50273200-50277000	Weak transcription	Fetal Intestine Small	intestine
38	chr13:50273200-50278800	Weak transcription	A549	lung
39	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
40	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr13:50273400-50278200	Weak transcription	Fetal Stomach	stomach
42	chr13:50274000-50276800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr13:50274000-50277400	Strong transcription	Fetal Intestine Large	intestine
44	chr13:50274000-50277600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr13:50274000-50286600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr13:50274200-50276800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr13:50274200-50277000	Strong transcription	Fetal Thymus	thymus
48	chr13:50274200-50277200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr13:50274200-50286400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr13:50274200-50286400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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