Variant report

Variant	rs12914570
Chromosome Location	chr15:42970899-42970900
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	chr15:42957477..42963934-chr15:42964860..42973083,9	K562	blood:
2	chr15:42969516..42971199-chr15:42979000..42981438,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159433	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10162939	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs10518779	0.90[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs1058846	0.83[CEU][hapmap]
rs1197550	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs1197551	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12102055	0.85[CEU][hapmap]
rs12594855	0.83[CEU][hapmap]
rs12902830	0.83[CEU][hapmap]
rs12905385	0.84[CEU][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap]
rs12906497	0.80[CEU][hapmap]
rs12911585	0.89[CEU][hapmap]
rs12912064	0.81[ASN][1000 genomes]
rs16957020	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs16957043	0.90[YRI][hapmap]
rs16957168	0.90[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs1705356	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs17774047	0.83[CEU][hapmap]
rs1995939	0.85[CEU][hapmap]
rs2136899	0.85[ASW][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.87[MKK][hapmap]
rs2136900	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs2175370	0.89[CEU][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap]
rs2280048	0.84[CEU][hapmap]
rs2305084	0.80[CEU][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap]
rs28542286	0.84[ASN][1000 genomes]
rs3099758	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs3199486	0.85[CEU][hapmap]
rs3742993	0.93[ASW][hapmap];0.89[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.83[YRI][hapmap]
rs4545789	0.89[CEU][hapmap];0.90[YRI][hapmap]
rs4924690	1.00[CEU][hapmap]
rs4924691	1.00[CEU][hapmap]
rs4924692	0.89[CEU][hapmap]
rs4924694	0.86[GIH][hapmap]
rs623271	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs6493059	0.86[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap]
rs672054	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs67391479	0.81[ASN][1000 genomes]
rs7163030	0.94[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap]
rs7166373	0.89[CEU][hapmap]
rs7167392	0.80[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap]
rs7169009	0.85[CEU][hapmap]
rs7169202	0.94[CEU][hapmap]
rs7175582	0.80[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs7182141	0.80[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs7182515	0.90[JPT][hapmap]
rs8023524	0.84[CEU][hapmap]
rs8024902	0.89[CEU][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap]
rs8028785	0.90[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs8030587	0.83[CEU][hapmap]
rs8031218	0.83[CEU][hapmap]
rs8039711	0.89[CEU][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap]
rs8039765	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs8043472	1.00[CEU][hapmap]
rs9269	0.89[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap]
rs938047	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs9919994	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs9920163	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap]
rs9920202	0.90[JPT][hapmap]

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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv517553	chr15:42970899-43023482	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12914570	BUB1B	cis	parietal	SCAN
rs12914570	SPTBN5	cis	cerebellum	SCAN
rs12914570	TGM5	cis	lymphoblastoid	seeQTL
rs12914570	CDAN1	cis	parietal	SCAN
rs12914570	SPINT1	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
2	chr15:42928200-42973600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:42928200-42974000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:42942800-42973600	Weak transcription	Psoas Muscle	Psoas
5	chr15:42945200-42973400	Weak transcription	Thymus	Thymus
6	chr15:42949800-42999200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr15:42950400-42990200	Strong transcription	Fetal Stomach	stomach
8	chr15:42951000-42995000	Strong transcription	Fetal Muscle Trunk	muscle
9	chr15:42952200-42973400	Weak transcription	Gastric	stomach
10	chr15:42952600-42979000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:42952600-42995600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:42952800-42996000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:42953400-42992200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:42954200-42973600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:42954400-42976200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:42954600-42986200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr15:42954800-42983000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:42955000-42990200	Strong transcription	Fetal Muscle Leg	muscle
19	chr15:42955200-42974000	Weak transcription	Esophagus	oesophagus
20	chr15:42956000-42976400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:42956800-42973600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:42957000-42976200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:42960000-42973400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:42960000-42981800	Strong transcription	Primary T cells from cord blood	blood
25	chr15:42960200-42973800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:42961000-42977600	Weak transcription	Small Intestine	intestine
27	chr15:42961200-42973800	Weak transcription	Fetal Thymus	thymus
28	chr15:42961200-42989200	Strong transcription	Ovary	ovary
29	chr15:42961400-42990800	Strong transcription	Colon Smooth Muscle	Colon
30	chr15:42961600-42989200	Weak transcription	Pancreas	Pancrea
31	chr15:42961800-42975000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:42962000-42974000	Weak transcription	HSMMtube	muscle
33	chr15:42963800-42976200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:42964200-42982400	Weak transcription	A549	lung
35	chr15:42964600-42972200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:42964600-42972800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:42964600-42979200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr15:42965000-42982200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:42966000-42972400	Strong transcription	Placenta	Placenta
40	chr15:42966000-42992800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:42966200-42972000	Strong transcription	Lung	lung
42	chr15:42966200-42972200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:42966400-42978400	Weak transcription	Dnd41	blood
44	chr15:42966400-42988400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:42966400-42988600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:42966600-42972200	Strong transcription	Rectal Smooth Muscle	rectum
47	chr15:42966600-42979400	Strong transcription	Spleen	Spleen
48	chr15:42966600-42979800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:42966600-42982400	Strong transcription	Fetal Brain Female	brain
50	chr15:42966600-42982800	Strong transcription	Primary hematopoietic stem cells	blood

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