Variant report

Variant	rs4558798
Chromosome Location	chr3:98308915-98308916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98306181..98309113-chr3:98310458..98312557,3	K562	blood:
2	chr3:98302949..98305459-chr3:98308547..98310946,2	K562	blood:
3	chr3:98307277..98308985-chr3:98312690..98314425,2	K562	blood:

Variant related genes	Relation type
ENSG00000080819	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10222524	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1350792	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1350793	0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1381090	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1675526	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1675527	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1675528	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1675531	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1729978	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1729980	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1729995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2698315	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34330560	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3762654	0.89[EUR][1000 genomes]
rs3853723	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv997484	chr3:98284283-98371420	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1000357	chr3:98284283-98381473	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv536661	chr3:98286588-98315764	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4558798	ST3GAL6	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98287200-98310200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:98287400-98310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:98292400-98310400	Weak transcription	Small Intestine	intestine
4	chr3:98292400-98311000	Weak transcription	Fetal Brain Male	brain
5	chr3:98292600-98310200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:98293000-98311800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:98293200-98310400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:98294400-98310400	Weak transcription	Colonic Mucosa	Colon
9	chr3:98294400-98311000	Weak transcription	Stomach Mucosa	stomach
10	chr3:98294800-98311000	Weak transcription	Esophagus	oesophagus
11	chr3:98295600-98309800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:98296000-98310200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:98296200-98310400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:98296400-98310000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:98296600-98311200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:98296800-98309600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:98296800-98310800	Weak transcription	NHLF	lung
18	chr3:98297000-98309600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:98297400-98310400	Weak transcription	Hela-S3	cervix
20	chr3:98298200-98310800	Weak transcription	HUVEC	blood vessel
21	chr3:98299600-98309000	Weak transcription	Lung	lung
22	chr3:98299600-98311200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:98300000-98311200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:98301800-98310000	Strong transcription	Liver	Liver
25	chr3:98302000-98309800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:98302400-98310000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr3:98302400-98310200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:98302600-98309600	Strong transcription	Fetal Thymus	thymus
29	chr3:98302600-98310200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:98302600-98310200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:98303000-98309400	Strong transcription	Fetal Stomach	stomach
32	chr3:98303600-98310000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr3:98303800-98310200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:98304000-98309000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:98304400-98311600	Weak transcription	Aorta	Aorta
36	chr3:98304600-98309000	Weak transcription	Pancreas	Pancrea
37	chr3:98304600-98310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:98304600-98310000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:98304600-98310600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:98304600-98310800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:98304600-98311400	Weak transcription	HSMMtube	muscle
42	chr3:98304800-98310000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:98304800-98310200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:98304800-98311000	Weak transcription	HSMM	muscle
45	chr3:98305000-98311600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:98305200-98311000	Weak transcription	Spleen	Spleen
47	chr3:98305200-98311600	Weak transcription	Gastric	stomach
48	chr3:98305400-98310000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:98305400-98311000	Weak transcription	Thymus	Thymus
50	chr3:98305600-98311000	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links