Variant report

Variant	rs12898997
Chromosome Location	chr15:75090349-75090350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75090308-75092006	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:75090055-75093409	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:75090180-75093445	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:75089967-75094280	GM12892	blood:	n/a	n/a
5	POLR2A	chr15:75090180-75090625	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:75089866-75092958	GM12892	blood:	n/a	n/a
7	POLR2A	chr15:75090205-75090538	GM12878	blood:	n/a	n/a
8	MTA3	chr15:75089924-75092899	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75090293-75090615	GM12891	blood:	n/a	n/a
10	POLR2A	chr15:75089848-75095044	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:75090169-75094342	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74907410..74909925-chr15:75089055..75090678,2	MCF-7	breast:
2	chr15:75088510..75091913-chr15:75102419..75105144,4	K562	blood:
3	chr15:75079725..75083728-chr15:75089989..75095483,10	MCF-7	breast:

Variant related genes	Relation type
CSK	TF binding region
ENSG00000260919	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000264386	Chromatin interaction
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11072507	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11072508	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11630478	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632414	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11635664	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12591513	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594062	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12903541	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12903896	0.82[AMR][1000 genomes]
rs12905199	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909307	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12917376	0.98[ASN][1000 genomes]
rs1378940	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378941	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1378942	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2168518	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470890	0.82[AMR][1000 genomes]
rs2472304	0.82[AMR][1000 genomes]
rs2960192	0.84[AMR][1000 genomes]
rs34862454	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35206230	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784789	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886410	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62006567	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12898997	SCAMP5	cis	lung	GTEx
rs12898997	SCAMP5	cis	Artery Tibial	GTEx
rs12898997	COX5A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75077800-75092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:75079400-75093800	Weak transcription	Aorta	Aorta
3	chr15:75081200-75091400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:75081800-75092000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:75081800-75092000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr15:75082200-75092200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:75082400-75098400	Weak transcription	Fetal Kidney	kidney
8	chr15:75082600-75090400	Weak transcription	HepG2	liver
9	chr15:75082600-75093200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:75083000-75090400	Weak transcription	Dnd41	blood
11	chr15:75083000-75092000	Weak transcription	Hela-S3	cervix
12	chr15:75083000-75093000	Weak transcription	HUVEC	blood vessel
13	chr15:75083200-75090400	Weak transcription	Fetal Brain Female	brain
14	chr15:75083200-75091800	Weak transcription	A549	lung
15	chr15:75083200-75092400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:75083200-75093600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr15:75083400-75090600	Weak transcription	Fetal Lung	lung
18	chr15:75083800-75091600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:75084400-75093200	Genic enhancers	Primary B cells from cord blood	blood
20	chr15:75084400-75094600	Weak transcription	HSMMtube	muscle
21	chr15:75084800-75091000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:75085200-75090600	Weak transcription	Psoas Muscle	Psoas
23	chr15:75085200-75091400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:75085600-75091800	Weak transcription	NHDF-Ad	bronchial
25	chr15:75085800-75091800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr15:75085800-75091800	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:75085800-75093200	Weak transcription	Ovary	ovary
28	chr15:75086000-75090400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr15:75086000-75090400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:75086000-75090400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:75086000-75090600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:75086000-75090600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:75086000-75090600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:75086000-75090800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:75086000-75091400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:75086000-75091600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr15:75086000-75092200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr15:75086000-75092200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr15:75086000-75092200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:75086000-75092800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:75086000-75093600	Genic enhancers	Primary B cells from peripheral blood	blood
42	chr15:75086000-75093800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:75086000-75094200	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr15:75086000-75107400	Weak transcription	Fetal Brain Male	brain
45	chr15:75086200-75090400	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr15:75086200-75090600	Weak transcription	Brain Angular Gyrus	brain
47	chr15:75086200-75090800	Weak transcription	Brain Hippocampus Middle	brain
48	chr15:75086200-75091800	Weak transcription	Osteobl	bone
49	chr15:75086200-75093200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:75086200-75093200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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