Variant report

Variant	rs12909307
Chromosome Location	chr15:75061929-75061930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:74926428..74928297-chr15:75060418..75062112,2	K562	blood:
2	chr15:75061714..75065079-chr15:75242940..75246213,4	K562	blood:
3	chr15:74924667..74926194-chr15:75061014..75063397,2	MCF-7	breast:
4	chr15:75060913..75062896-chr15:75196962..75199239,2	K562	blood:
5	chr15:74933224..74935053-chr15:75061299..75063816,2	MCF-7	breast:
6	chr15:75056268..75058478-chr15:75059962..75062607,3	K562	blood:
7	chr15:75060561..75062896-chr15:75196962..75199741,2	K562	blood:
8	chr15:74933237..74935346-chr15:75060041..75062599,2	K562	blood:
9	chr15:74922603..74925094-chr15:75061118..75062996,2	MCF-7	breast:
10	chr15:75061295..75062973-chr15:75074582..75077010,2	K562	blood:
11	chr15:74921493..74922466-chr15:75061289..75062251,2	MCF-7	breast:
12	chr15:75051545..75054051-chr15:75061447..75064196,2	K562	blood:
13	chr15:74925800..74926609-chr15:75061536..75062096,2	MCF-7	breast:
14	chr15:75056268..75058478-chr15:75059962..75062462,2	K562	blood:
15	chr15:74921154..74924652-chr15:75061303..75063546,3	K562	blood:
16	chr15:74926277..74928672-chr15:75060421..75062184,32	K562	blood:
17	chr15:74926309..74927880-chr15:75061284..75064051,2	MCF-7	breast:
18	chr15:74926605..74928994-chr15:75060559..75063448,5	MCF-7	breast:
19	chr15:74906941..74909010-chr15:75059898..75062184,2	MCF-7	breast:
20	chr15:74907408..74909628-chr15:75059869..75062492,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000179335	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000179151	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	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11630478	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11632414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635664	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12591513	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12594062	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12898997	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903541	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12903896	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12905199	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12917376	0.91[ASN][1000 genomes]
rs1378940	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378941	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1378942	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2168518	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470890	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2472304	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2960192	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34862454	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35206230	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3784789	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886410	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62006567	0.81[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
rs12909307	SCAMP5	cis	lung	GTEx
rs12909307	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12909307	SCAMP5	cis	Artery Tibial	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75044800-75062600	Weak transcription	Right Atrium	heart
2	chr15:75047200-75063000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:75055200-75063200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:75055600-75065800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:75056000-75069000	Weak transcription	Lung	lung
6	chr15:75056200-75063200	Weak transcription	Spleen	Spleen
7	chr15:75061200-75063000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:75061200-75063200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr15:75061200-75063400	Weak transcription	Brain Substantia Nigra	brain
10	chr15:75061400-75062400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:75061400-75062600	Weak transcription	HepG2	liver
12	chr15:75061400-75062800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:75061400-75063200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:75061400-75063200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:75061400-75063200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:75061400-75063200	Weak transcription	Brain Anterior Caudate	brain
17	chr15:75061400-75063200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr15:75061400-75063400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:75061400-75063400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:75061400-75063400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:75061400-75063400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:75061400-75063400	Weak transcription	Thymus	Thymus
23	chr15:75061400-75063400	Weak transcription	Dnd41	blood
24	chr15:75061400-75063400	Weak transcription	HMEC	breast
25	chr15:75061400-75064000	Weak transcription	HUVEC	blood vessel
26	chr15:75061400-75064200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr15:75061400-75065600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:75061400-75069000	Weak transcription	Liver	Liver
29	chr15:75061600-75063200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr15:75061600-75063200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:75061600-75063200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:75061600-75063200	Weak transcription	Fetal Thymus	thymus
33	chr15:75061600-75063400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr15:75061800-75063400	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links