Variant report

Variant	rs12892246
Chromosome Location	chr14:31815634-31815635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:31675418..31678639-chr14:31811864..31816181,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092148	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10147938	0.96[EUR][1000 genomes]
rs11626839	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap]
rs12886167	0.86[EUR][1000 genomes]
rs12886725	0.86[EUR][1000 genomes]
rs12895352	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17577629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17660791	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17660955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2146570	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap]
rs2181420	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2182252	0.83[EUR][1000 genomes]
rs2182253	0.84[EUR][1000 genomes]
rs34159200	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34737578	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34777795	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35330064	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35335466	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35474202	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35628255	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35952505	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3736917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41496248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs4981832	0.90[ASN][1000 genomes]
rs4981841	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[LWK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61994183	0.86[EUR][1000 genomes]
rs61995529	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61995554	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61996784	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs727671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs927704	0.85[EUR][1000 genomes];0.90[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	esv2830427	chr14:31639110-32000034	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1050597	chr14:31711248-31904761	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv901589	chr14:31768231-31944723	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12892246	HEATR5A	cis	cerebellum	SCAN
rs12892246	EGLN3	cis	cerebellum	SCAN
rs12892246	RP11-176H8.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31771000-31888800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr14:31772400-31825200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr14:31782200-31875200	Weak transcription	Gastric	stomach
4	chr14:31782400-31827000	Weak transcription	Aorta	Aorta
5	chr14:31799600-31827000	Weak transcription	Right Ventricle	heart
6	chr14:31799800-31829600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr14:31799800-31866800	Weak transcription	Esophagus	oesophagus
8	chr14:31800200-31839800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr14:31800400-31838200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr14:31801200-31823400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr14:31801200-31883800	Weak transcription	Small Intestine	intestine
12	chr14:31801400-31862800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr14:31801400-31875600	Weak transcription	Brain Germinal Matrix	brain
14	chr14:31801600-31824000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr14:31801600-31872400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr14:31801800-31824400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr14:31801800-31862600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:31802400-31825000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr14:31802400-31827200	Weak transcription	Brain Substantia Nigra	brain
20	chr14:31802400-31842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr14:31802600-31825000	Weak transcription	GM12878-XiMat	blood
22	chr14:31802800-31872000	Weak transcription	Fetal Brain Male	brain
23	chr14:31803400-31817600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr14:31803600-31825000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr14:31803600-31833000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr14:31803600-31872600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr14:31803800-31843600	Weak transcription	A549	lung
28	chr14:31803800-31852200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr14:31804000-31825000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr14:31805600-31816400	Weak transcription	Fetal Stomach	stomach
31	chr14:31805600-31825000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr14:31805600-31851800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:31806000-31819600	Strong transcription	HSMM	muscle
34	chr14:31806200-31850800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr14:31806400-31825400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr14:31806400-31829200	Strong transcription	Placenta	Placenta
37	chr14:31806600-31826600	Weak transcription	NHEK	skin
38	chr14:31806600-31826800	Weak transcription	Hela-S3	cervix
39	chr14:31807000-31815800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr14:31807400-31825400	Weak transcription	Psoas Muscle	Psoas
41	chr14:31808000-31872600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr14:31808600-31827000	Weak transcription	Lung	lung
43	chr14:31808800-31818200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr14:31809600-31824600	Weak transcription	Pancreas	Pancrea
45	chr14:31809600-31872000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr14:31810200-31816000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr14:31810200-31822200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr14:31810200-31827800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr14:31810400-31823200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr14:31810400-31823600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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