Variant report

Variant	rs1049532
Chromosome Location	chr5:178510048-178510049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10038484	0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10057660	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10063310	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10067183	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10068311	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10072631	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10479525	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1562233	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1562234	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2161170	0.81[AMR][1000 genomes]
rs34320394	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3797590	0.92[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs3797615	0.92[CEU][hapmap]
rs3822591	0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes]
rs4700780	0.87[CEU][hapmap]
rs4701032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701035	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4701036	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4701037	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs4701038	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4701040	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4701041	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4701042	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4701043	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4701046	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4701048	0.92[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes]
rs62393088	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6864241	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6868661	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6877691	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs716782	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7727747	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7728180	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1027487	chr5:178455495-178510587	Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv482750	chr5:178482653-178663586	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1023392	chr5:178495775-178516483	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv1021642	chr5:178495775-178535309	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1028000	chr5:178500527-178516483	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1015745	chr5:178503162-178519187	ZNF genes & repeats Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv1823858	chr5:178507069-178515895	ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv600491	chr5:178507090-178515853	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1049532	RAB24	cis	parietal	SCAN
rs1049532	DKFZp686E2433	Cis_1M	lymphoblastoid	RTeQTL
rs1049532	ZNF454	cis	parietal	SCAN
rs1049532	DDX41	cis	cerebellum	SCAN
rs1049532	ZNF879	cis	cerebellum	SCAN
rs1049532	DOK3	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178488200-178511000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:178488400-178511600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:178488400-178512000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:178488600-178517200	ZNF genes & repeats	Liver	Liver
5	chr5:178489400-178511400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr5:178490600-178517400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:178492600-178512200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
8	chr5:178492600-178513400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
9	chr5:178492800-178511200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:178492800-178517200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:178492800-178517200	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr5:178498400-178511000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
13	chr5:178498600-178511400	ZNF genes & repeats	Brain Germinal Matrix	brain
14	chr5:178498600-178512000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:178498600-178512000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:178500600-178511800	ZNF genes & repeats	Fetal Brain Female	brain
17	chr5:178500600-178512400	ZNF genes & repeats	Brain Substantia Nigra	brain
18	chr5:178500800-178511200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
19	chr5:178502600-178511200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr5:178502600-178511200	ZNF genes & repeats	Psoas Muscle	Psoas
21	chr5:178502800-178511200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
22	chr5:178503000-178510600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:178503000-178511000	ZNF genes & repeats	Fetal Kidney	kidney
24	chr5:178507800-178511400	ZNF genes & repeats	Aorta	Aorta
25	chr5:178507800-178512200	ZNF genes & repeats	Left Ventricle	heart
26	chr5:178508000-178510200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:178508600-178511600	ZNF genes & repeats	Right Ventricle	heart
28	chr5:178508800-178511600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
29	chr5:178509200-178511200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
30	chr5:178509200-178511200	ZNF genes & repeats	Ovary	ovary
31	chr5:178509200-178512200	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr5:178509600-178510200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:178509600-178510200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:178509600-178510200	ZNF genes & repeats	Placenta	Placenta
35	chr5:178509600-178510200	ZNF genes & repeats	Lung	lung
36	chr5:178509600-178510200	ZNF genes & repeats	Pancreas	Pancrea
37	chr5:178509600-178510400	ZNF genes & repeats	Brain Anterior Caudate	brain
38	chr5:178509600-178510800	ZNF genes & repeats	Colon Smooth Muscle	Colon
39	chr5:178509600-178511200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:178509600-178511400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:178509600-178512000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:178509600-178512000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
43	chr5:178509600-178512000	ZNF genes & repeats	Fetal Lung	lung
44	chr5:178509600-178512200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:178509600-178512200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
46	chr5:178509600-178512200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr5:178509600-178512400	ZNF genes & repeats	Brain Hippocampus Middle	brain
48	chr5:178509600-178512400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
49	chr5:178509600-178512400	ZNF genes & repeats	HSMM	muscle
50	chr5:178509800-178510200	ZNF genes & repeats	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links