Variant report

Variant	rs2245588
Chromosome Location	chr5:94878263-94878264
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	chr5:94877399..94880074-chr5:94889020..94891541,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164291	Chromatin interaction
ENSG00000198677	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10053324	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10076499	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1183640	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1541798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1981952	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2545841	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2548652	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2560257	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560260	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2560261	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2560274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2731825	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2731826	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2731833	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2881976	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6556870	0.85[ASN][1000 genomes]
rs73777211	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9314148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2245588	TTC37	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94811000-94889400	Weak transcription	Stomach Mucosa	stomach
2	chr5:94818000-94882400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:94825000-94886200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:94825400-94886400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:94826000-94886400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr5:94826800-94886400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr5:94827200-94889600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:94828800-94885800	Strong transcription	Fetal Thymus	thymus
9	chr5:94835200-94881000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:94841400-94883400	Strong transcription	Primary B cells from cord blood	blood
11	chr5:94841800-94886000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr5:94842000-94884800	Strong transcription	Dnd41	blood
13	chr5:94842200-94882000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:94842200-94886000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr5:94845600-94879800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:94846600-94881000	Weak transcription	Gastric	stomach
17	chr5:94847400-94890000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:94849200-94890000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:94849800-94879800	Weak transcription	Fetal Stomach	stomach
20	chr5:94849800-94881400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:94850600-94879200	Weak transcription	Small Intestine	intestine
22	chr5:94851800-94881200	Weak transcription	Right Ventricle	heart
23	chr5:94853800-94879800	Weak transcription	Lung	lung
24	chr5:94853800-94880400	Weak transcription	Pancreas	Pancrea
25	chr5:94853800-94890000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:94855800-94878400	Strong transcription	Liver	Liver
27	chr5:94857600-94884800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr5:94864400-94889400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:94865200-94880200	Weak transcription	Spleen	Spleen
30	chr5:94865200-94889400	Weak transcription	Esophagus	oesophagus
31	chr5:94865200-94890000	Weak transcription	Aorta	Aorta
32	chr5:94866000-94880200	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:94866400-94880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:94866600-94881000	Weak transcription	NHEK	skin
35	chr5:94867400-94880800	Weak transcription	Fetal Heart	heart
36	chr5:94867400-94886000	Strong transcription	Adipose Nuclei	Adipose
37	chr5:94867600-94879200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:94868400-94879200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:94868800-94886000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:94869400-94883000	Strong transcription	Primary hematopoietic stem cells	blood
41	chr5:94869400-94889000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:94869600-94878400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr5:94869600-94883200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:94869800-94881400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr5:94870000-94883000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:94870000-94886200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:94870200-94885800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:94870200-94889000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:94870400-94879200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:94870400-94879400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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