Variant report

Variant	rs1505289
Chromosome Location	chr3:24411856-24411857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24404057..24405809-chr3:24411604..24413512,2	K562	blood:
2	chr3:24408664..24412376-chr3:24534339..24537876,4	MCF-7	breast:
3	chr3:24404154..24407745-chr3:24409924..24412829,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11129150	0.83[EUR][1000 genomes]
rs11129152	0.85[ASN][1000 genomes]
rs11918018	0.84[ASN][1000 genomes]
rs12495379	0.81[CEU][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13065876	0.81[ASN][1000 genomes]
rs13086388	0.84[ASN][1000 genomes]
rs1394761	0.80[AMR][1000 genomes]
rs1505286	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1505287	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17014597	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17014605	0.81[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2135147	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs28380451	0.81[ASN][1000 genomes]
rs35340172	0.82[ASN][1000 genomes]
rs4276128	0.81[EUR][1000 genomes]
rs4300958	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4309672	0.84[ASN][1000 genomes]
rs4602332	0.80[ASN][1000 genomes]
rs4630886	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4858608	0.80[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs4858610	0.84[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs6550865	0.81[JPT][hapmap]
rs6769978	0.84[ASN][1000 genomes]
rs6771995	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7611219	0.81[JPT][hapmap]
rs7630858	0.85[ASN][1000 genomes]
rs9310739	0.82[EUR][1000 genomes]
rs9310740	0.81[CEU][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9816509	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9826887	0.83[EUR][1000 genomes]
rs9851523	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs9852824	0.81[CEU][hapmap];0.82[TSI][hapmap];0.83[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	nsv834640	chr3:24339779-24493605	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1505289	NKIRAS1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24360400-24418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:24394000-24431400	Weak transcription	Gastric	stomach
3	chr3:24407400-24418400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:24407800-24412000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:24407800-24414400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:24407800-24414600	Weak transcription	Fetal Kidney	kidney
7	chr3:24408000-24412000	Weak transcription	NHDF-Ad	bronchial
8	chr3:24408800-24412000	Enhancers	Rectal Smooth Muscle	rectum
9	chr3:24409200-24416400	Weak transcription	A549	lung
10	chr3:24409400-24412000	Enhancers	Colon Smooth Muscle	Colon
11	chr3:24409400-24412000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:24409400-24414400	Weak transcription	Fetal Lung	lung
13	chr3:24409400-24415000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:24409600-24414800	Weak transcription	Liver	Liver
15	chr3:24410000-24414600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:24410200-24413600	Weak transcription	HepG2	liver
17	chr3:24410200-24414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:24410200-24414800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:24410400-24412000	Weak transcription	Stomach Mucosa	stomach
20	chr3:24410400-24414400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:24410800-24412200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:24411000-24412000	Enhancers	Aorta	Aorta
23	chr3:24411200-24412200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:24411400-24412600	Enhancers	Fetal Intestine Small	intestine
25	chr3:24411800-24412200	Enhancers	Fetal Intestine Large	intestine
26	chr3:24411800-24412200	Enhancers	Left Ventricle	heart
27	chr3:24411800-24412400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:24411800-24412400	Enhancers	Pancreas	Pancrea
29	chr3:24411800-24412400	Enhancers	Psoas Muscle	Psoas
30	chr3:24411800-24412400	Enhancers	Right Atrium	heart
31	chr3:24411800-24413400	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links