Variant report

Variant	rs12909335
Chromosome Location	chr15:75214789-75214790
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75205785..75208557-chr15:75213491..75215641,2	MCF-7	breast:
2	chr15:75196885..75199275-chr15:75214478..75217231,2	K562	blood:
3	chr15:75213925..75215879-chr15:75227652..75232134,4	MCF-7	breast:
4	chr15:75193756..75196013-chr15:75211451..75215315,3	K562	blood:

Variant related genes	Relation type
ENSG00000178741	Chromatin interaction
ENSG00000178761	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11072511	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs11072512	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127796	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1130741	0.96[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs1133322	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1133323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630087	0.80[AMR][1000 genomes]
rs11630592	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11630918	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11633472	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636892	0.80[AMR][1000 genomes]
rs11638130	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11639413	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11854704	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11856413	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11857695	0.83[EUR][1000 genomes]
rs12148513	0.83[AFR][1000 genomes]
rs12487	0.84[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap]
rs12898539	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12899430	0.81[EUR][1000 genomes]
rs12899787	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12900662	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12901190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902515	0.83[EUR][1000 genomes]
rs12903205	0.85[EUR][1000 genomes]
rs12903370	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904326	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904897	0.89[EUR][1000 genomes]
rs12907898	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12908365	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12911254	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12912343	0.81[AMR][1000 genomes]
rs12912839	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913293	0.87[EUR][1000 genomes]
rs12914217	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1378942	1.00[LWK][hapmap]
rs2044157	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168518	1.00[LWK][hapmap]
rs2290573	0.84[ASW][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap]
rs2415251	0.84[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34063670	0.81[AMR][1000 genomes]
rs34799293	0.80[AMR][1000 genomes]
rs35556055	0.81[CEU][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs35882241	0.81[AMR][1000 genomes]
rs4643278	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886413	0.80[AMR][1000 genomes]
rs4886608	0.82[EUR][1000 genomes]
rs4886632	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886636	0.92[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs4886639	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886640	0.92[EUR][1000 genomes]
rs4886649	0.84[ASW][hapmap]
rs59945415	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62029167	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62029217	0.80[AMR][1000 genomes]
rs6495122	0.85[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs7495664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495739	0.96[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs7497026	0.86[EUR][1000 genomes]
rs7497393	0.96[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8025447	0.88[EUR][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	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12909335	SCAMP2	cis	parietal	SCAN
rs12909335	SCAMP5	cis	Artery Tibial	GTEx
rs12909335	CSK	cis	lymphoblastoid	seeQTL
rs12909335	SCAMP2	cis	Whole Blood	GTEx
rs12909335	ULK3	cis	parietal	SCAN
rs12909335	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs12909335	TLE3	cis	cerebellum	SCAN
rs12909335	CYP1A1	cis	cerebellum	SCAN
rs12909335	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs12909335	MPI	cis	lymphoblastoid	seeQTL
rs12909335	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75199600-75229400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75199800-75219600	Weak transcription	Aorta	Aorta
3	chr15:75200000-75221000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:75200000-75224000	Weak transcription	Stomach Mucosa	stomach
5	chr15:75200400-75221200	Weak transcription	Fetal Heart	heart
6	chr15:75201000-75224600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:75202000-75224400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr15:75202200-75224400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:75202600-75224800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:75202600-75225000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:75203000-75224400	Strong transcription	Fetal Muscle Leg	muscle
12	chr15:75203000-75224600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:75203200-75222200	Strong transcription	Left Ventricle	heart
14	chr15:75203400-75218000	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:75203800-75223000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:75203800-75224200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr15:75203800-75224400	Strong transcription	Fetal Intestine Large	intestine
18	chr15:75203800-75224600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:75204000-75216600	Strong transcription	Thymus	Thymus
20	chr15:75204000-75217600	Strong transcription	Lung	lung
21	chr15:75204000-75220600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr15:75204000-75221800	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr15:75204000-75222200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:75204000-75222400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr15:75204000-75224200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:75204000-75224200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:75204000-75224400	Strong transcription	Placenta	Placenta
28	chr15:75204000-75224600	Strong transcription	Liver	Liver
29	chr15:75204000-75224600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:75204000-75224800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:75204000-75224800	Strong transcription	Fetal Thymus	thymus
32	chr15:75204000-75228400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:75204200-75224200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:75204400-75224600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr15:75204600-75229200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:75205400-75216600	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr15:75205600-75222000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:75205600-75223200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr15:75206000-75216200	Strong transcription	A549	lung
40	chr15:75206200-75222200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:75206200-75224400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:75206400-75217800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr15:75206400-75224200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:75206600-75221800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:75206800-75224600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:75207000-75216600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:75207000-75217400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr15:75207000-75217600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:75207000-75225800	Strong transcription	Hela-S3	cervix
50	chr15:75207200-75216200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links