Variant report

Variant	rs1160121
Chromosome Location	chr5:90001988-90001989
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89992042..89994832-chr5:90000512..90002853,2	K562	blood:
2	chr5:89989350..89991740-chr5:90000493..90002123,2	K562	blood:
3	chr5:89989350..89991740-chr5:89999562..90002123,3	K562	blood:
4	chr5:89998991..90003482-chr5:90003758..90009177,7	K562	blood:
5	chr5:89996062..89998352-chr5:90001342..90003176,2	K562	blood:
6	chr5:90001746..90003482-chr5:90003758..90005802,2	K562	blood:
7	chr5:89704471..89707067-chr5:89999894..90001997,2	K562	blood:
8	chr5:90001172..90003183-chr5:90006013..90008402,2	K562	blood:
9	chr5:89996062..89999170-chr5:90000730..90003176,4	K562	blood:
10	chr5:89992042..89994832-chr5:90000512..90002853,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000255647	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10036980	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10043836	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10045236	0.87[ASN][1000 genomes]
rs10058765	1.00[JPT][hapmap]
rs10060365	0.81[ASN][1000 genomes]
rs10060427	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10062714	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10062924	1.00[JPT][hapmap]
rs10067181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10068473	0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs10072105	0.92[JPT][hapmap]
rs1014750	0.87[ASN][1000 genomes]
rs1028191	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1028192	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1033290	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1033291	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10514327	0.92[JPT][hapmap]
rs10514333	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10942597	0.85[JPT][hapmap]
rs10942605	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942606	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12188928	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12516985	1.00[JPT][hapmap]
rs12655180	0.82[JPT][hapmap]
rs12657264	0.87[ASN][1000 genomes]
rs13153584	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13167491	0.87[ASN][1000 genomes]
rs13185955	0.85[JPT][hapmap]
rs1533603	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1673378	0.84[JPT][hapmap]
rs1673379	0.92[JPT][hapmap]
rs16868957	1.00[JPT][hapmap]
rs1700510	0.83[JPT][hapmap]
rs1700511	0.92[JPT][hapmap]
rs1878878	0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1993474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2176624	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2222242	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2366771	0.92[JPT][hapmap]
rs2366773	0.91[JPT][hapmap]
rs2366774	0.83[JPT][hapmap]
rs2366777	1.00[JPT][hapmap]
rs28587199	0.89[ASN][1000 genomes]
rs3805483	0.92[JPT][hapmap]
rs3927265	0.86[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs490812	0.92[JPT][hapmap]
rs4916681	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4916684	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4916686	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4916813	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4916815	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs498491	0.92[JPT][hapmap]
rs499148	0.85[JPT][hapmap]
rs502596	0.92[JPT][hapmap]
rs603015	0.85[JPT][hapmap]
rs617379	0.92[JPT][hapmap]
rs618355	0.83[JPT][hapmap]
rs637442	0.92[JPT][hapmap]
rs6452904	0.89[ASN][1000 genomes]
rs6452905	0.89[ASN][1000 genomes]
rs6452906	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs645652	0.92[JPT][hapmap]
rs648430	0.85[JPT][hapmap]
rs6861525	0.83[ASN][1000 genomes]
rs6863710	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs6878917	0.92[JPT][hapmap]
rs6881412	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6883872	0.91[JPT][hapmap]
rs6888355	0.91[JPT][hapmap]
rs688956	0.92[JPT][hapmap];0.82[TSI][hapmap]
rs688960	0.92[JPT][hapmap]
rs6898209	1.00[JPT][hapmap]
rs7703588	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7714506	0.89[ASN][1000 genomes]
rs7721198	1.00[JPT][hapmap]
rs7723259	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7724806	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7726624	0.92[JPT][hapmap]
rs7729703	1.00[JPT][hapmap]
rs7732169	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9293550	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs963866	1.00[JPT][hapmap]
rs977906	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9790907	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv934323	chr5:89968158-90111853	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv882368	chr5:89990324-90012379	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1031718	chr5:89999033-90099868	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1160121	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL
rs1160121	POLR3G	cis	cerebellum	SCAN
rs1160121	LYSMD3	cis	normal skin	skin_eQTL
rs1160121	GPR98	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89950400-90033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:89979200-90002600	Weak transcription	Brain Anterior Caudate	brain
3	chr5:89982000-90004600	Weak transcription	Fetal Brain Female	brain
4	chr5:89987800-90007200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr5:89991800-90014000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:89995000-90025800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:89997800-90017600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:89998800-90018000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:89999200-90002200	Strong transcription	K562	blood
10	chr5:89999600-90010000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:89999800-90004200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:90001200-90002000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:90001200-90002200	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr5:90001200-90002400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr5:90001600-90002200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:90001600-90002200	Strong transcription	Brain Germinal Matrix	brain
17	chr5:90001800-90006000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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