Variant report

Variant	rs2366777
Chromosome Location	chr5:89943571-89943572
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89823962..89827222-chr5:89937926..89943647,5	K562	blood:
2	chr5:89703250..89710229-chr5:89936398..89944611,13	K562	blood:
3	chr5:89938651..89940282-chr5:89943212..89946172,3	MCF-7	breast:

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

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10036258	0.81[EUR][1000 genomes]
rs10036980	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10043836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10045236	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10058765	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10060427	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10062714	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10062924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10067181	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs10068473	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10072105	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1014750	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1028191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1028192	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1033290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10462342	0.92[JPT][hapmap]
rs10514327	0.92[JPT][hapmap]
rs10514333	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10942596	0.85[JPT][hapmap]
rs10942597	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10942605	1.00[JPT][hapmap]
rs10942606	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1160121	1.00[JPT][hapmap]
rs11741740	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12187830	0.92[ASN][1000 genomes]
rs12188928	1.00[JPT][hapmap]
rs12516985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12652606	0.83[EUR][1000 genomes]
rs12655180	0.82[JPT][hapmap]
rs12657264	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13167491	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13185955	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1533603	1.00[CEU][hapmap];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];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16868957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1700510	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs1700511	0.92[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17554723	0.84[ASW][hapmap]
rs1878878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1988788	0.90[ASN][1000 genomes]
rs1993474	1.00[JPT][hapmap]
rs2176624	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2222242	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2366771	1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs2366773	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2366774	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2366928	1.00[ASW][hapmap]
rs2460177	1.00[ASW][hapmap]
rs28517617	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28550273	0.97[ASN][1000 genomes]
rs28587199	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3805483	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs3927265	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4379236	0.97[ASN][1000 genomes]
rs4574581	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs474800	0.80[ASN][1000 genomes]
rs490812	0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs491241	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4916681	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4916682	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916686	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4916813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916814	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916815	1.00[JPT][hapmap]
rs498491	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs499148	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs502596	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]
rs552314	0.80[ASN][1000 genomes]
rs603015	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs617379	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs618355	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs623761	0.80[ASN][1000 genomes]
rs637442	0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6452904	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6452905	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6452906	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs645652	1.00[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs648430	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6861525	0.90[ASN][1000 genomes]
rs6863710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6878917	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6881412	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6883872	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6888355	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs688956	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs688960	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6898209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7703530	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7703588	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7714506	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7721198	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7723259	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7724806	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7726624	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7729703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7732169	0.96[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9283788	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9293550	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs963866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9790907	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2366777	LYSMD3	cis	normal skin	skin_eQTL
rs2366777	GPR98	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89918000-89950600	Weak transcription	Pancreas	Pancrea
2	chr5:89929000-89948600	Weak transcription	Brain Anterior Caudate	brain
3	chr5:89936600-89949000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:89936600-89951000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:89936800-89948600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:89936800-89951000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:89936800-89994200	Weak transcription	Brain Germinal Matrix	brain
8	chr5:89937000-89948600	Weak transcription	Fetal Brain Female	brain
9	chr5:89941400-89948600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:89941400-89957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:89941600-89947400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:89941600-89949000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:89941600-89951600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:89941600-89954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:89941800-89957600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:89942400-89944600	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr5:89942400-89944600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:89942400-89944800	Transcr. at gene 5' and 3'	K562	blood
19	chr5:89942400-89945400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:89942400-89947400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:89942800-89944600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr5:89942800-89950200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:89943000-89944600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:89943000-89946000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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