Variant report

Variant	rs502596
Chromosome Location	chr5:89901315-89901316
allele	C/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	chr5:89900781..89902890-chr5:89944313..89947231,2	K562	blood:
2	chr5:89899238..89902193-chr5:89950994..89956361,5	K562	blood:
3	chr5:89883022..89885296-chr5:89901095..89903175,2	K562	blood:
4	chr5:89704196..89707423-chr5:89899106..89902473,4	K562	blood:
5	chr5:89853355..89855789-chr5:89900091..89901923,2	MCF-7	breast:
6	chr5:89899642..89902183-chr5:89950994..89955309,3	K562	blood:
7	chr5:89824298..89826504-chr5:89901067..89902762,2	MCF-7	breast:
8	chr5:89767614..89772956-chr5:89898929..89905987,8	K562	blood:
9	chr5:89900245..89902488-chr5:89903253..89905685,5	K562	blood:
10	chr5:89823952..89826315-chr5:89899219..89901608,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000113356	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10036980	0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap]
rs10043836	0.92[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs10058765	0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10060427	0.93[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10062714	0.93[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10062924	0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs10067181	0.92[JPT][hapmap]
rs10068473	0.92[JPT][hapmap]
rs10072105	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1028191	1.00[ASW][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1028192	1.00[ASW][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs1033290	0.93[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10462342	0.84[JPT][hapmap]
rs10473936	0.87[ASN][1000 genomes]
rs10514327	0.84[JPT][hapmap]
rs10514328	0.83[ASN][1000 genomes]
rs10514333	0.91[JPT][hapmap]
rs10942597	0.92[JPT][hapmap]
rs10942605	0.92[JPT][hapmap]
rs10942606	0.85[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap]
rs1160121	0.92[JPT][hapmap]
rs11741740	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12187830	0.82[ASN][1000 genomes]
rs12188928	0.92[JPT][hapmap]
rs12516985	0.92[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs13185955	0.92[JPT][hapmap]
rs1533603	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs1673378	0.92[JPT][hapmap]
rs1673379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16868957	0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1700510	0.93[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs1700511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17554723	0.84[ASW][hapmap]
rs1878878	1.00[ASW][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs1993474	0.92[JPT][hapmap]
rs2176624	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs2222242	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs2366771	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2366773	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2366774	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2366777	1.00[ASW][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2366928	1.00[ASW][hapmap]
rs2460177	1.00[ASW][hapmap]
rs28517617	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28550273	0.86[ASN][1000 genomes]
rs3805483	0.84[JPT][hapmap]
rs3927265	0.81[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap]
rs4379236	0.86[ASN][1000 genomes]
rs4574581	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs474800	0.89[ASN][1000 genomes]
rs490812	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs491241	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916681	0.93[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs4916682	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916684	0.93[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4916686	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs4916813	0.93[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916814	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916815	0.91[JPT][hapmap]
rs498491	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs499148	0.92[JPT][hapmap]
rs501640	0.86[ASN][1000 genomes]
rs552314	0.89[ASN][1000 genomes]
rs587818	0.85[ASN][1000 genomes]
rs603015	0.92[JPT][hapmap]
rs617379	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618355	0.92[JPT][hapmap]
rs623761	0.89[ASN][1000 genomes]
rs637442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6452906	0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap]
rs645652	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs648430	0.92[JPT][hapmap]
rs666659	0.87[ASN][1000 genomes]
rs6863710	0.93[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6870337	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6878917	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6881412	1.00[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap]
rs6883872	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6888355	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688956	0.82[ASW][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs688960	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6891275	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6897910	0.84[JPT][hapmap]
rs6898209	1.00[ASW][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7703530	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7703588	0.92[JPT][hapmap]
rs7721198	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7723259	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs7724806	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs7726624	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7729703	0.93[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7732169	0.92[JPT][hapmap]
rs9283788	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9293550	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs963866	0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs977906	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9790907	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs502596	GPR98	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89892800-89909000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:89893000-89907800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:89893200-89902000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:89895000-89907400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:89899600-89902000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:89900400-89903200	Enhancers	K562	blood
7	chr5:89900800-89902600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:89901000-89908200	Weak transcription	GM12878-XiMat	blood

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