Variant report

Variant	rs10043564
Chromosome Location	chr5:89950272-89950273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:89950102..89952185-chr5:89967907..89971424,3	K562	blood:
2	chr5:89921820..89923590-chr5:89949531..89951597,2	K562	blood:

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10037067	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs10040165	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs10064606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs10942604	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs11958484	0.94[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12186867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12653924	0.95[CEU][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1316970	0.81[ASN][1000 genomes]
rs1474119	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs1474120	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs149321	0.96[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1568308	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1673381	1.00[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs16868980	0.95[CHB][hapmap]
rs16868999	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs16869010	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs16869042	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs16876822	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs2366772	0.96[CEU][hapmap];0.81[JPT][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2366775	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2366926	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs250366	0.83[JPT][hapmap]
rs257847	0.96[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap]
rs27196	0.80[JPT][hapmap]
rs27197	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs3112773	0.96[EUR][1000 genomes]
rs4588621	0.96[CEU][hapmap];0.82[JPT][hapmap];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4916685	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs5028525	0.96[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs599432	0.85[JPT][hapmap]
rs62375083	0.92[ASN][1000 genomes]
rs649449	0.96[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs656679	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs6861067	0.83[ASW][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap]
rs6880239	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs6891840	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6892132	0.96[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7716829	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs908818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9293549	0.81[ASN][1000 genomes]
rs970319	0.95[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
6	nsv933161	chr5:89939500-89954066	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv1029970	chr5:89940489-89986831	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv1032225	chr5:89940489-89999954	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv1025391	chr5:89943364-89995164	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv537805	chr5:89943364-89995164	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS 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
rs10043564	GPR98	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89918000-89950600	Weak transcription	Pancreas	Pancrea
2	chr5:89936600-89951000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:89936800-89951000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:89936800-89994200	Weak transcription	Brain Germinal Matrix	brain
5	chr5:89941400-89957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:89941600-89951600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:89941600-89954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:89941800-89957600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:89944800-89956600	Weak transcription	Fetal Brain Male	brain
10	chr5:89945400-89951800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:89945800-89950400	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr5:89948000-89955400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:89948000-89955800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:89948400-89950800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:89948600-89950800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:89949000-89950400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:89949600-89951400	Weak transcription	Brain Anterior Caudate	brain
18	chr5:89949600-89954600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:89949600-89964000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:89949800-89952600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:89950000-89950800	Transcr. at gene 5' and 3'	K562	blood
22	chr5:89950200-89953200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:89950200-89953800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:89950200-89954400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:89950200-89981600	Weak transcription	Fetal Brain Female	brain

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