Variant report

Variant	rs3805483
Chromosome Location	chr5:89803587-89803588
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	chr5:89803083..89805276-chr5:89823748..89825574,3	K562	blood:
2	chr5:89801527..89803796-chr5:89803997..89806887,2	K562	blood:

Variant related genes	Relation type
ENSG00000176018	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10043836	0.92[JPT][hapmap]
rs10058765	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs10060427	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs10062714	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs10062924	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs10068473	0.92[JPT][hapmap]
rs10072105	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs1028191	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs1028192	0.92[JPT][hapmap]
rs1033290	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs10462342	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1047787	0.90[ASN][1000 genomes]
rs10514327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10514333	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10942596	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10942597	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs10942605	0.92[JPT][hapmap]
rs10942606	0.92[JPT][hapmap]
rs1160121	0.92[JPT][hapmap]
rs11743030	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12188928	0.92[JPT][hapmap]
rs12516985	0.91[JPT][hapmap]
rs12655180	1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs13182165	0.87[ASN][1000 genomes]
rs13185955	1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs1673378	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs1673379	0.84[JPT][hapmap]
rs16868957	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs1700510	0.81[CHB][hapmap]
rs1700511	0.84[JPT][hapmap]
rs1812737	0.88[ASN][1000 genomes]
rs1878878	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs2176624	0.92[JPT][hapmap]
rs2366771	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2366773	0.82[JPT][hapmap]
rs2366774	0.81[CHB][hapmap]
rs2366777	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs3087840	0.90[ASN][1000 genomes]
rs35407205	1.00[ASN][1000 genomes]
rs490812	0.84[JPT][hapmap]
rs4916681	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs4916684	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs4916813	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs498491	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs499148	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs502596	0.84[JPT][hapmap]
rs558809	0.83[ASN][1000 genomes]
rs603015	1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs603870	0.88[ASN][1000 genomes]
rs616379	0.88[ASN][1000 genomes]
rs617379	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs618355	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs637442	0.84[JPT][hapmap]
rs645652	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs648430	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs67376567	1.00[ASN][1000 genomes]
rs6863710	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs6878917	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6883872	0.82[JPT][hapmap]
rs6888355	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs688956	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs688960	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs6897910	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.89[ASN][1000 genomes]
rs6898209	0.92[JPT][hapmap]
rs72781084	0.86[ASN][1000 genomes]
rs7712128	0.93[EUR][1000 genomes]
rs7717423	0.88[ASN][1000 genomes]
rs7721198	0.90[JPT][hapmap]
rs7726624	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7729703	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs963866	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs977906	0.92[JPT][hapmap]
rs9790907	0.81[CHB][hapmap];0.84[JPT][hapmap]

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	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882364	chr5:89748142-89808531	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3805483	GPR98	cis	cerebellum	SCAN
rs3805483	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89771600-89814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:89773800-89816000	Weak transcription	HepG2	liver
3	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:89774000-89814600	Weak transcription	Dnd41	blood
5	chr5:89774400-89814600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:89777000-89806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:89780400-89810800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr5:89783800-89813400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:89784800-89814600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:89785400-89814600	Weak transcription	NHLF	lung
12	chr5:89790200-89809600	Weak transcription	GM12878-XiMat	blood
13	chr5:89791400-89814600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:89791600-89813800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:89791600-89814600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:89792200-89810400	Weak transcription	Left Ventricle	heart
17	chr5:89793800-89823400	Weak transcription	Hela-S3	cervix
18	chr5:89797600-89814600	Weak transcription	Adipose Nuclei	Adipose
19	chr5:89797600-89824200	Weak transcription	Brain Angular Gyrus	brain
20	chr5:89798000-89814600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:89799600-89805200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:89799600-89817200	Weak transcription	NHDF-Ad	bronchial
23	chr5:89799800-89814600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:89800000-89807600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:89800000-89814400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:89800000-89814600	Weak transcription	NHEK	skin
27	chr5:89800800-89808200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:89800800-89808600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr5:89800800-89811600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:89800800-89814600	Weak transcription	HMEC	breast
31	chr5:89801000-89813600	Weak transcription	NH-A	brain
32	chr5:89801000-89814600	Weak transcription	HUVEC	blood vessel
33	chr5:89801200-89809200	Weak transcription	A549	lung
34	chr5:89802000-89807000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:89802200-89804600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:89802400-89803800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:89802600-89824600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:89803000-89804000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:89803000-89805200	Weak transcription	K562	blood
40	chr5:89803200-89805200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr5:89803200-89810400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr5:89803200-89817600	Weak transcription	Small Intestine	intestine

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