Variant report

Variant	rs498435
Chromosome Location	chr4:130032031-130032032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:130019234..130021165-chr4:130030871..130032869,2	K562	blood:
2	chr4:130017343..130020226-chr4:130031173..130032927,2	K562	blood:
3	chr4:130030784..130034303-chr4:130034493..130036505,5	K562	blood:
4	chr4:130028612..130032885-chr4:130034533..130038076,4	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10014640	0.80[JPT][hapmap]
rs10028124	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10857134	0.82[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12650832	0.90[CEU][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13132428	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1450727	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699390	0.95[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1699396	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1709416	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1709417	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757941	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs175964	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1947269	1.00[ASW][hapmap];0.90[CEU][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2218814	0.95[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2592953	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2592955	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2592956	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs280592	0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs280598	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs280600	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs280602	0.95[CEU][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2893267	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3099898	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3119696	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs318538	0.83[JPT][hapmap]
rs318540	0.84[JPT][hapmap]
rs318542	0.81[JPT][hapmap]
rs318544	0.81[JPT][hapmap]
rs318546	0.81[JPT][hapmap]
rs318548	0.80[JPT][hapmap]
rs318549	0.80[JPT][hapmap]
rs318554	0.84[JPT][hapmap]
rs318562	0.81[JPT][hapmap]
rs318564	0.81[JPT][hapmap]
rs337264	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs337265	0.85[CHB][hapmap]
rs4165	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975192	0.85[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4975287	1.00[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975288	0.82[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4975289	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4975290	0.95[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4975291	1.00[ASW][hapmap];0.90[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975292	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs536631	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs62316963	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62318666	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6814109	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6817901	0.95[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6820403	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6820637	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6821814	1.00[ASW][hapmap];0.95[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6830229	0.94[CEU][hapmap];0.89[JPT][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6840358	0.81[JPT][hapmap]
rs7691218	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs789986	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs498435	FLJ30655	cis	multi-tissue	Pritchard
rs498435	HSPA4L	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130017600-130040400	Weak transcription	Lung	lung
2	chr4:130017800-130032600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:130017800-130032800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:130017800-130033400	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:130017800-130033400	Weak transcription	Thymus	Thymus
6	chr4:130017800-130034200	Weak transcription	Colonic Mucosa	Colon
7	chr4:130018000-130032400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:130018000-130033000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:130018000-130033200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:130018000-130033400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr4:130018000-130034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:130018000-130038000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr4:130018200-130032400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:130018800-130033800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:130023600-130033400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr4:130025200-130033200	Weak transcription	Fetal Lung	lung
17	chr4:130025400-130032200	Weak transcription	Fetal Brain Male	brain
18	chr4:130025800-130035000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:130026800-130032200	Weak transcription	Placenta	Placenta
20	chr4:130028400-130033600	Weak transcription	Fetal Brain Female	brain
21	chr4:130028800-130032200	Weak transcription	NHDF-Ad	bronchial
22	chr4:130028800-130032400	Weak transcription	Brain Anterior Caudate	brain
23	chr4:130028800-130036600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:130029200-130032600	Weak transcription	HSMMtube	muscle
25	chr4:130029200-130040000	Weak transcription	Esophagus	oesophagus
26	chr4:130029400-130035400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:130029400-130041200	Weak transcription	Spleen	Spleen
28	chr4:130029600-130038600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:130029800-130033000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:130030200-130032200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:130030200-130032400	Strong transcription	Primary T cells from cord blood	blood
32	chr4:130030200-130032400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr4:130030200-130032400	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:130030400-130032200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr4:130030400-130032200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:130030400-130032200	Strong transcription	Adipose Nuclei	Adipose
37	chr4:130030400-130032400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr4:130030400-130032400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:130030400-130033600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:130030400-130034000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:130030600-130032200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr4:130030600-130032400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:130030600-130032400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:130030600-130032400	Strong transcription	Liver	Liver
45	chr4:130030600-130032400	Enhancers	Fetal Heart	heart
46	chr4:130030800-130034000	Weak transcription	NHEK	skin
47	chr4:130030800-130035600	Weak transcription	Gastric	stomach
48	chr4:130031000-130032200	Strong transcription	Fetal Thymus	thymus
49	chr4:130031400-130032200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:130031400-130032200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links