Variant report

Variant	rs688956
Chromosome Location	chr5:89863279-89863280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89862796..89864795-chr5:89866978..89869006,2	K562	blood:
2	chr5:89854805..89859362-chr5:89860971..89864483,4	K562	blood:
3	chr5:89851829..89860351-chr5:89861712..89870170,13	K562	blood:

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10036980	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs10043836	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs10058765	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10060427	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10062714	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10062924	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10067181	0.92[JPT][hapmap]
rs10068473	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs10072105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1028191	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1028192	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1033290	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs10462342	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs10473936	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1047787	0.82[EUR][1000 genomes]
rs10514327	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs10514328	0.88[ASN][1000 genomes]
rs10514333	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs10942597	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs10942605	0.92[JPT][hapmap];0.82[TSI][hapmap]
rs10942606	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1160121	0.92[JPT][hapmap];0.82[TSI][hapmap]
rs11741740	0.94[ASN][1000 genomes]
rs12188928	0.92[JPT][hapmap]
rs12516985	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs13182165	0.85[EUR][1000 genomes]
rs13185955	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1533603	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1673378	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1673379	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16868957	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs1700510	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1700511	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1812737	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1878878	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1993474	0.92[JPT][hapmap]
rs2176624	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2222242	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2366771	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2366773	0.82[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2366774	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2366777	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs2366928	0.82[ASW][hapmap]
rs2460177	0.82[ASW][hapmap]
rs28550273	0.84[ASN][1000 genomes]
rs3087840	0.82[EUR][1000 genomes]
rs3805483	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs3927265	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs4379236	0.84[ASN][1000 genomes]
rs474800	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490812	0.92[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs491241	0.91[ASN][1000 genomes]
rs4916681	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs4916682	0.80[ASN][1000 genomes]
rs4916684	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4916686	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4916813	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs4916814	0.80[ASN][1000 genomes]
rs4916815	0.91[JPT][hapmap]
rs498491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs499148	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs501640	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs502596	0.82[ASW][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs552314	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558809	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs587818	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs603015	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs603870	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs616379	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs617379	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs618355	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs623761	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637442	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6452906	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs645652	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs648430	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs666659	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6863710	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6878917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6881412	0.82[ASW][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs6883872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6888355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs688960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6897910	1.00[CEU][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6898209	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs7703588	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs7716979	0.82[EUR][1000 genomes]
rs7717423	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7721198	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7723259	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs7724806	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7726624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7729703	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs7732169	0.92[JPT][hapmap]
rs9283788	0.83[ASN][1000 genomes]
rs9293550	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs963866	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs977906	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs9790907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[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	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
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs688956	GPR98	cis	cerebellum	SCAN
rs688956	LYSMD3	cis	normal skin	skin_eQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89855200-89871000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:89859400-89864200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:89859400-89884200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:89860200-89868000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:89862000-89864400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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