Variant report

Variant	rs11854704
Chromosome Location	chr15:75221015-75221016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75219083..75221777-chr15:75225866..75227747,2	K562	blood:
2	chr15:75210612..75213940-chr15:75219994..75223601,6	K562	blood:
3	chr15:75219020..75222087-chr15:75227777..75231704,4	K562	blood:
4	chr15:75197679..75199782-chr15:75220402..75222080,2	MCF-7	breast:
5	chr15:75219020..75221811-chr15:75227777..75230276,3	K562	blood:
6	chr15:75220124..75223006-chr15:75247944..75250326,2	MCF-7	breast:
7	chr15:75219486..75222765-chr15:75228648..75231849,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178718	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000178741	Chromatin interaction
ENSG00000198794	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11072511	0.92[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs11072512	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072513	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072514	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1127796	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1130741	0.96[CEU][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs1133322	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[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133323	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11630918	0.92[CEU][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs11633472	0.84[ASW][hapmap];0.96[CEU][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11638130	0.84[ASW][hapmap];0.96[CEU][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11639413	0.80[EUR][1000 genomes]
rs11856413	0.84[ASW][hapmap];0.96[CEU][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11857695	0.88[EUR][1000 genomes]
rs12487	0.89[CEU][hapmap]
rs12898539	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12899430	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12899787	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900662	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12901190	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12902515	0.88[EUR][1000 genomes]
rs12903205	0.90[EUR][1000 genomes]
rs12903370	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12904326	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12904897	0.96[EUR][1000 genomes]
rs12907898	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908365	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909335	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]
rs12912839	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12913293	0.91[EUR][1000 genomes]
rs12914217	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044157	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2415251	0.96[CEU][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs35556055	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs4643278	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886608	0.90[EUR][1000 genomes]
rs4886632	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4886636	0.92[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs4886639	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59945415	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62029167	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495122	0.85[CEU][hapmap]
rs7495664	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7495739	0.96[CEU][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs7497026	0.90[EUR][1000 genomes]
rs7497393	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs8025447	0.92[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11854704	ULK3	cis	parietal	SCAN
rs11854704	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs11854704	MPI	cis	lymphoblastoid	seeQTL
rs11854704	SCAMP5	cis	Artery Tibial	GTEx
rs11854704	SCAMP2	cis	parietal	SCAN
rs11854704	ZNF572	trans	cerebellum	SCAN
rs11854704	SCAMP2	cis	Esophagus Mucosa	GTEx
rs11854704	CYP11A1	cis	cerebellum	SCAN
rs11854704	TLE3	cis	cerebellum	SCAN
rs11854704	SCAMP2	cis	Whole Blood	GTEx
rs11854704	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs11854704	ETFA	cis	cerebellum	SCAN

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	chr15:75200000-75224000	Weak transcription	Stomach Mucosa	stomach
3	chr15:75200400-75221200	Weak transcription	Fetal Heart	heart
4	chr15:75201000-75224600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:75202000-75224400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr15:75202200-75224400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:75202600-75224800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:75202600-75225000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:75203000-75224400	Strong transcription	Fetal Muscle Leg	muscle
10	chr15:75203000-75224600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:75203200-75222200	Strong transcription	Left Ventricle	heart
12	chr15:75203800-75223000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:75203800-75224200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr15:75203800-75224400	Strong transcription	Fetal Intestine Large	intestine
15	chr15:75203800-75224600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:75204000-75221800	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:75204000-75222200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:75204000-75222400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:75204000-75224200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:75204000-75224200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:75204000-75224400	Strong transcription	Placenta	Placenta
22	chr15:75204000-75224600	Strong transcription	Liver	Liver
23	chr15:75204000-75224600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:75204000-75224800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:75204000-75224800	Strong transcription	Fetal Thymus	thymus
26	chr15:75204000-75228400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:75204200-75224200	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr15:75204400-75224600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr15:75204600-75229200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr15:75205600-75222000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr15:75205600-75223200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:75206200-75222200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:75206200-75224400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:75206400-75224200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:75206600-75221800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:75206800-75224600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:75207000-75225800	Strong transcription	Hela-S3	cervix
38	chr15:75207200-75224200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:75207200-75224400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:75207800-75227400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:75209200-75224600	Strong transcription	Adipose Nuclei	Adipose
42	chr15:75209400-75221600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr15:75209400-75224600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:75209600-75222400	Strong transcription	Dnd41	blood
45	chr15:75209800-75222000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:75212400-75229600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:75212600-75229200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr15:75212800-75224200	Strong transcription	Fetal Intestine Small	intestine
49	chr15:75212800-75224200	Strong transcription	Fetal Stomach	stomach
50	chr15:75212800-75226000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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