Variant report

Variant	rs17082398
Chromosome Location	chr4:53987764-53987765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53987651..53991411-chr4:53993052..53996048,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10028181	0.83[JPT][hapmap]
rs1038355	0.82[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.83[EUR][1000 genomes]
rs10517275	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs11133243	0.83[JPT][hapmap]
rs11732744	0.85[EUR][1000 genomes]
rs11931066	0.84[EUR][1000 genomes]
rs11934112	0.81[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.85[EUR][1000 genomes]
rs11947923	0.82[GIH][hapmap]
rs12506298	0.85[EUR][1000 genomes]
rs2046306	0.84[EUR][1000 genomes]
rs2046307	0.82[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs28770187	0.87[EUR][1000 genomes]
rs3849654	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4241973	0.83[JPT][hapmap]
rs4302515	0.81[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4314341	0.84[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4320191	1.00[ASW][hapmap];0.81[CEU][hapmap];0.88[GIH][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4479763	0.85[EUR][1000 genomes]
rs4864723	0.80[YRI][hapmap]
rs59629308	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66506011	0.85[ASN][1000 genomes]
rs6811236	0.85[EUR][1000 genomes]
rs6822251	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs6843335	0.82[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.84[EUR][1000 genomes]
rs6846933	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs6847431	0.82[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs72624189	0.86[EUR][1000 genomes]
rs72624190	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72624191	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7378381	0.82[JPT][hapmap]
rs7662427	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs7676982	0.82[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap]
rs998264	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17082398	KIT	cis	parietal	SCAN
rs17082398	CLIC6	trans	parietal	SCAN
rs17082398	HOPX	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53978800-54008000	Weak transcription	Primary T cells from cord blood	blood
2	chr4:53980400-53993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:53982200-53989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:53984800-53989600	Enhancers	Brain Substantia Nigra	brain
5	chr4:53985200-53988200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:53985600-53988000	Enhancers	Osteobl	bone
7	chr4:53985600-53989600	Enhancers	Fetal Intestine Small	intestine
8	chr4:53985600-53990200	Enhancers	Stomach Mucosa	stomach
9	chr4:53985600-53991400	Enhancers	HepG2	liver
10	chr4:53985800-53987800	Enhancers	NHLF	lung
11	chr4:53985800-53988600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:53985800-53988800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:53985800-53988800	Enhancers	Right Atrium	heart
14	chr4:53985800-53989000	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr4:53985800-53989600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:53985800-53989600	Enhancers	Fetal Lung	lung
17	chr4:53986000-53987800	Enhancers	Adipose Nuclei	Adipose
18	chr4:53986000-53989400	Enhancers	Brain Anterior Caudate	brain
19	chr4:53986200-53993000	Weak transcription	Fetal Stomach	stomach
20	chr4:53986200-53993200	Weak transcription	Fetal Kidney	kidney
21	chr4:53986200-53993600	Weak transcription	Psoas Muscle	Psoas
22	chr4:53986600-53988200	Weak transcription	Colonic Mucosa	Colon
23	chr4:53986600-53989800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:53986600-53993600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:53986600-53994600	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:53986800-53988400	Weak transcription	Fetal Intestine Large	intestine
27	chr4:53986800-53989600	Weak transcription	Placenta	Placenta
28	chr4:53986800-53990000	Enhancers	Brain Hippocampus Middle	brain
29	chr4:53986800-53990400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr4:53986800-54010800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:53986800-54011000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:53987000-53987800	Weak transcription	NHDF-Ad	bronchial
33	chr4:53987200-53988400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:53987200-53988600	Enhancers	Brain Cingulate Gyrus	brain
35	chr4:53987200-53989000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:53987400-53987800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:53987400-53988000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:53987400-53988000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:53987400-53988000	Enhancers	Left Ventricle	heart
40	chr4:53987400-53988000	Enhancers	Ovary	ovary
41	chr4:53987400-53989000	Enhancers	Brain Angular Gyrus	brain
42	chr4:53987400-53989800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:53987400-53990200	Enhancers	Small Intestine	intestine
44	chr4:53987600-53987800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:53987600-53987800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:53987600-53987800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr4:53987600-53987800	Enhancers	Aorta	Aorta
48	chr4:53987600-53991200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:53987600-53993600	Weak transcription	Fetal Muscle Leg	muscle

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