Variant report

Variant	rs4864723
Chromosome Location	chr4:53986846-53986847
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	chr4:53978972..53981461-chr4:53984171..53987382,3	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10026738	0.89[GIH][hapmap]
rs12508105	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13118742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17082398	0.80[YRI][hapmap]
rs2411290	0.89[GIH][hapmap];0.87[MEX][hapmap]
rs2887235	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3849654	0.80[YRI][hapmap]
rs4320191	0.80[YRI][hapmap]
rs7684453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991167	0.89[GIH][hapmap];0.91[MEX][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4864723	SPINK2	cis	parietal	SCAN

Chromatin state (count:46 , 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	chr4:53983200-53987400	Weak transcription	Ovary	ovary
5	chr4:53984800-53989600	Enhancers	Brain Substantia Nigra	brain
6	chr4:53985200-53988200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr4:53985600-53987000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:53985600-53987000	Enhancers	NHDF-Ad	bronchial
9	chr4:53985600-53987200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:53985600-53988000	Enhancers	Osteobl	bone
11	chr4:53985600-53989600	Enhancers	Fetal Intestine Small	intestine
12	chr4:53985600-53990200	Enhancers	Stomach Mucosa	stomach
13	chr4:53985600-53991400	Enhancers	HepG2	liver
14	chr4:53985800-53987600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr4:53985800-53987800	Enhancers	NHLF	lung
16	chr4:53985800-53988600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:53985800-53988800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:53985800-53988800	Enhancers	Right Atrium	heart
19	chr4:53985800-53989000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr4:53985800-53989600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:53985800-53989600	Enhancers	Fetal Lung	lung
22	chr4:53986000-53987800	Enhancers	Adipose Nuclei	Adipose
23	chr4:53986000-53989400	Enhancers	Brain Anterior Caudate	brain
24	chr4:53986200-53987200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:53986200-53987400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:53986200-53993000	Weak transcription	Fetal Stomach	stomach
27	chr4:53986200-53993200	Weak transcription	Fetal Kidney	kidney
28	chr4:53986200-53993600	Weak transcription	Psoas Muscle	Psoas
29	chr4:53986400-53987000	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:53986400-53987400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:53986400-53987400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr4:53986600-53987000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:53986600-53987600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:53986600-53988200	Weak transcription	Colonic Mucosa	Colon
35	chr4:53986600-53989800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr4:53986600-53993600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:53986600-53994600	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:53986800-53987200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:53986800-53987200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:53986800-53987200	Enhancers	Aorta	Aorta
41	chr4:53986800-53988400	Weak transcription	Fetal Intestine Large	intestine
42	chr4:53986800-53989600	Weak transcription	Placenta	Placenta
43	chr4:53986800-53990000	Enhancers	Brain Hippocampus Middle	brain
44	chr4:53986800-53990400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:53986800-54010800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:53986800-54011000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links