Variant report

Variant	rs42467
Chromosome Location	chr5:89853069-89853070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:89851855-89854488	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89822684..89827061-chr5:89851623..89857043,7	MCF-7	breast:
2	chr5:89852793..89854346-chr5:89883740..89885331,2	MCF-7	breast:
3	chr5:89768685..89771799-chr5:89852676..89855842,6	MCF-7	breast:
4	chr5:89830924..89832784-chr5:89851773..89854511,2	K562	blood:
5	chr5:89721701..89723836-chr5:89852631..89854336,2	K562	blood:
6	chr5:89845076..89846894-chr5:89852308..89854212,2	K562	blood:
7	chr5:89838541..89840104-chr5:89852722..89854353,2	K562	blood:
8	chr5:89769141..89770698-chr5:89851659..89854573,2	K562	blood:
9	chr5:89769550..89772254-chr5:89851679..89856622,6	MCF-7	breast:
10	chr5:89704746..89707502-chr5:89851587..89854165,2	K562	blood:
11	chr5:89704382..89708328-chr5:89852696..89856618,6	MCF-7	breast:

No data

Variant related genes	Relation type
GPR98	TF binding region
ENSG00000176018	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10069050	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12653924	0.82[JPT][hapmap]
rs149321	0.86[JPT][hapmap]
rs154568	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154569	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs154570	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154572	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs154573	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1553545	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1673381	0.86[JPT][hapmap]
rs171790	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2366772	0.85[JPT][hapmap]
rs2366775	0.82[JPT][hapmap]
rs250366	0.86[JPT][hapmap]
rs250377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs257847	0.86[JPT][hapmap]
rs257850	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs257851	0.92[EUR][1000 genomes]
rs2656957	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27196	0.95[JPT][hapmap]
rs27197	0.86[JPT][hapmap]
rs27201	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs37238	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs37239	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs37240	0.84[EUR][1000 genomes]
rs43149	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4588621	0.86[JPT][hapmap]
rs491082	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5028525	0.86[JPT][hapmap]
rs511393	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs526806	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs556894	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59159252	0.97[ASN][1000 genomes]
rs594990	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs599432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs625135	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs649449	0.86[JPT][hapmap]
rs656679	0.86[JPT][hapmap]
rs679568	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6884154	0.81[EUR][1000 genomes]
rs6892132	0.86[JPT][hapmap]
rs790081	0.83[CHD][hapmap]
rs810974	0.91[EUR][1000 genomes];0.81[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	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	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
8	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs42467	LYSMD3	cis	normal skin	skin_eQTL
rs42467	GPR98	cis	parietal	SCAN
rs42467	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL
rs42467	GPR98	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89843400-89853200	Weak transcription	Brain Anterior Caudate	brain
2	chr5:89844200-89853200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:89844200-89853400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:89844400-89853200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:89846200-89853200	Weak transcription	K562	blood
6	chr5:89849000-89853400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:89849200-89853200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:89850400-89853400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:89851600-89853200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr5:89852000-89853200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:89852200-89853200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:89852600-89853800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:89852600-89853800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr5:89852800-89853200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr5:89852800-89853200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:89852800-89853400	Enhancers	Brain Germinal Matrix	brain
17	chr5:89852800-89853600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
18	chr5:89852800-89853800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
19	chr5:89852800-89854000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr5:89853000-89853400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr5:89853000-89853400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
22	chr5:89853000-89853600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links