Variant report

Variant	rs37241
Chromosome Location	chr5:89853342-89853343
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
2	HA-E2F1	chr5:89853294-89855215	MCF-7	breast:	n/a	chr5:89854878-89854888 chr5:89854868-89854883 chr5:89854685-89854694 chr5:89854828-89854837
3	TCF7L2	chr5:89853185-89853361	PANC-1	pancreas:	n/a	chr5:89853316-89853326 chr5:89853211-89853220
4	MXI1	chr5:89853143-89855264	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr5:89853149-89855170	H1-hESC	embryonic stem cell:	n/a	n/a
6	KAP1	chr5:89853271-89855084	U2OS	brain:	n/a	n/a
7	SIN3A	chr5:89853202-89855199	H1-hESC	embryonic stem cell:	n/a	chr5:89854777-89854790 chr5:89854625-89854639 chr5:89854214-89854224

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:

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

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs152715	0.85[YRI][hapmap]
rs2162987	0.85[YRI][hapmap]
rs6452886	0.82[YRI][hapmap]
rs6897490	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs37241	GPR98	cis	brain	BrainEAC

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89844200-89853400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:89849000-89853400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:89850400-89853400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:89852600-89853800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:89852600-89853800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr5:89852800-89853400	Enhancers	Brain Germinal Matrix	brain
7	chr5:89852800-89853600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
8	chr5:89852800-89853800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
9	chr5:89852800-89854000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr5:89853000-89853400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:89853000-89853400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
12	chr5:89853000-89853600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr5:89853200-89853400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:89853200-89853400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
15	chr5:89853200-89853400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:89853200-89853400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:89853200-89853400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:89853200-89853400	Enhancers	Brain Hippocampus Middle	brain
19	chr5:89853200-89853400	Enhancers	K562	blood
20	chr5:89853200-89853400	Bivalent Enhancer	NH-A	brain
21	chr5:89853200-89853600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
22	chr5:89853200-89853600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:89853200-89853600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:89853200-89853600	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr5:89853200-89853800	Active TSS	Fetal Brain Female	brain
26	chr5:89853200-89853800	Bivalent Enhancer	Fetal Intestine Large	intestine
27	chr5:89853200-89854000	Bivalent Enhancer	Fetal Lung	lung
28	chr5:89853200-89854200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:89853200-89855200	Active TSS	Fetal Brain Male	brain
30	chr5:89853200-89855600	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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