Variant report

Variant	rs10060427
Chromosome Location	chr5:89951112-89951113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89950917..89953812-chr5:89965739..89968417,3	K562	blood:
2	chr5:89950102..89952185-chr5:89967907..89971424,3	K562	blood:
3	chr5:89921820..89923590-chr5:89949531..89951597,2	K562	blood:
4	chr5:89950925..89957089-chr5:90674771..90680308,6	K562	blood:
5	chr5:89899238..89902193-chr5:89950994..89956361,5	K562	blood:
6	chr5:89948021..89949895-chr5:89950501..89953146,2	MCF-7	breast:
7	chr5:89899642..89902183-chr5:89950994..89955309,3	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10036980	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs10043836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10058765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062714	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067181	1.00[JPT][hapmap]
rs10068473	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10072105	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs1028191	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1028192	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1033290	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10462342	0.92[JPT][hapmap]
rs10514327	0.92[JPT][hapmap]
rs10514333	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10942596	0.85[JPT][hapmap]
rs10942597	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10942605	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs10942606	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1160121	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11741740	0.82[ASN][1000 genomes]
rs12187830	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12188928	1.00[CEU][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs12516985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655180	0.82[JPT][hapmap]
rs13185955	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1533603	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1673378	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs1673379	0.93[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs16868957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1700510	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1700511	0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1878878	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1988788	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1993474	0.82[ASW][hapmap];1.00[JPT][hapmap]
rs2176624	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2222242	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2366771	1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs2366773	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2366774	1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs2366777	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28517617	0.90[ASN][1000 genomes]
rs28550273	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587199	0.80[ASN][1000 genomes]
rs3805483	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs3927265	0.85[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs4379236	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574581	0.81[ASN][1000 genomes]
rs474800	0.84[ASN][1000 genomes]
rs490812	0.92[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs491241	0.83[ASN][1000 genomes]
rs4916681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916682	0.97[ASN][1000 genomes]
rs4916684	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4916686	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4916813	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4916814	0.97[ASN][1000 genomes]
rs4916815	1.00[JPT][hapmap]
rs498491	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs499148	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs502596	0.93[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs552314	0.84[ASN][1000 genomes]
rs603015	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs617379	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs618355	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs623761	0.84[ASN][1000 genomes]
rs637442	0.92[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6452904	0.80[ASN][1000 genomes]
rs6452905	0.80[ASN][1000 genomes]
rs6452906	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs645652	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs648430	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs666659	0.81[ASN][1000 genomes]
rs6861525	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6863710	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6878447	0.85[EUR][1000 genomes]
rs6878917	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6881412	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6883872	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs6888355	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs688956	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs688960	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6898209	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7703530	0.88[ASN][1000 genomes]
rs7703588	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7714506	0.80[ASN][1000 genomes]
rs7721198	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7723259	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7724806	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7726624	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs7729703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7732169	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs9283788	0.88[ASN][1000 genomes]
rs9293550	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs963866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs977906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9790907	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]

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
rs10060427	GPR98	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89936800-89994200	Weak transcription	Brain Germinal Matrix	brain
2	chr5:89941400-89957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:89941600-89951600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:89941600-89954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:89941800-89957600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:89944800-89956600	Weak transcription	Fetal Brain Male	brain
7	chr5:89945400-89951800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:89948000-89955400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:89948000-89955800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:89949600-89951400	Weak transcription	Brain Anterior Caudate	brain
11	chr5:89949600-89954600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:89949600-89964000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:89949800-89952600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:89950200-89953200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:89950200-89953800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:89950200-89954400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:89950200-89981600	Weak transcription	Fetal Brain Female	brain
18	chr5:89950400-89956600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:89950400-90033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:89950800-89951200	Genic enhancers	K562	blood
21	chr5:89950800-89964000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:89950800-89973800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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