Variant report

Variant	rs494024
Chromosome Location	chr11:34464748-34464749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:34459587..34461714-chr11:34462902..34466251,4	K562	blood:
2	chr11:34457898..34462665-chr11:34462877..34466618,6	MCF-7	breast:
3	chr11:34384171..34386808-chr11:34464497..34467600,3	K562	blood:
4	chr11:34463426..34466853-chr11:34467996..34471084,4	K562	blood:
5	chr11:34391709..34394417-chr11:34464245..34466019,2	K562	blood:
6	chr11:34460366..34463492-chr11:34463916..34466562,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121691	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1001179	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs10836230	0.85[CEU][hapmap]
rs10836234	0.85[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs11032654	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs11032695	0.85[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs11032718	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11032719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11032722	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11032723	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11032724	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11032726	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11032728	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11604331	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.95[ASN][1000 genomes]
rs1267468	1.00[YRI][hapmap]
rs12790145	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12797274	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[ASN][1000 genomes]
rs12797675	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12804506	0.88[CHD][hapmap];0.89[GIH][hapmap]
rs12804689	0.89[GIH][hapmap]
rs12807961	0.85[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap]
rs12808450	0.85[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap]
rs1408041	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1535719	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17269903	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17269931	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2146962	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2231821	0.85[ASN][1000 genomes]
rs2231825	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs2231828	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2420386	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2476504	1.00[JPT][hapmap]
rs34234992	0.85[ASN][1000 genomes]
rs34366473	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34901344	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs35495760	0.85[ASN][1000 genomes]
rs475043	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4756130	0.82[ASW][hapmap]
rs4756135	1.00[YRI][hapmap]
rs499406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs508370	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs511895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs524167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs533425	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55898107	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs560807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737254	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs494024	CAT	cis	cerebellum	SCAN
rs494024	CAT	cis	multi-tissue	Pritchard
rs494024	DEPDC7	cis	parietal	SCAN
rs494024	CAT	cis	lymphoblastoid	seeQTL
rs494024	CAT	cis	Whole Blood	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34461400-34472200	Weak transcription	Aorta	Aorta
2	chr11:34461400-34473200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:34461400-34482800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:34461600-34470200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:34461600-34471400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:34461800-34465400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:34461800-34469800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:34461800-34470200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:34461800-34471400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr11:34461800-34471400	Weak transcription	Placenta	Placenta
11	chr11:34461800-34471400	Weak transcription	HSMM	muscle
12	chr11:34461800-34471400	Weak transcription	NH-A	brain
13	chr11:34461800-34471400	Weak transcription	NHEK	skin
14	chr11:34461800-34472200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:34461800-34472200	Weak transcription	Esophagus	oesophagus
16	chr11:34461800-34472200	Weak transcription	Lung	lung
17	chr11:34461800-34485800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:34462000-34464800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:34462000-34465600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:34462000-34466000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr11:34462000-34467600	Weak transcription	Stomach Mucosa	stomach
22	chr11:34462000-34469200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:34462000-34469400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:34462000-34469400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:34462000-34469800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:34462000-34469800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:34462000-34470600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:34462000-34470800	Weak transcription	Brain Hippocampus Middle	brain
29	chr11:34462000-34470800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:34462000-34470800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:34462000-34470800	Weak transcription	Osteobl	bone
32	chr11:34462000-34471400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr11:34462000-34471400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:34462000-34471400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr11:34462000-34471400	Weak transcription	HUVEC	blood vessel
36	chr11:34462000-34471400	Weak transcription	NHLF	lung
37	chr11:34462000-34472200	Weak transcription	Fetal Stomach	stomach
38	chr11:34462000-34472200	Weak transcription	Right Ventricle	heart
39	chr11:34462000-34474600	Weak transcription	Fetal Brain Male	brain
40	chr11:34462000-34477600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:34462400-34466800	Weak transcription	Left Ventricle	heart
42	chr11:34462600-34465600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr11:34462600-34467400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:34462600-34467400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr11:34462600-34467800	Weak transcription	Gastric	stomach
46	chr11:34462600-34469200	Weak transcription	Primary T cells from cord blood	blood
47	chr11:34462600-34471000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr11:34462600-34471400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr11:34462800-34467400	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr11:34462800-34469200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links