Variant report

Variant	rs11720342
Chromosome Location	chr3:140647398-140647399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140646965..140650706-chr3:140659494..140663953,5	MCF-7	breast:
2	chr3:140645222..140647869-chr3:140659939..140662297,3	K562	blood:
3	chr3:140645748..140651447-chr3:140658379..140662815,6	MCF-7	breast:
4	chr3:140645140..140648440-chr3:140656551..140659391,3	K562	blood:

Variant related genes	Relation type
ENSG00000114120	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1047306	0.80[AFR][1000 genomes]
rs1047330	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1056126	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1056127	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935413	0.89[ASN][1000 genomes]
rs10935414	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1109282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1109283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11707116	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710204	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11710926	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11711131	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11713505	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11713816	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs11714438	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715248	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717097	0.93[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11717620	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11718040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718539	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs11718563	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489397	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs13063450	0.84[ASN][1000 genomes]
rs13099706	0.84[ASN][1000 genomes]
rs1568337	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1593624	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16850915	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16850917	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16850921	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16850924	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16850926	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2081662	0.84[ASN][1000 genomes]
rs2292919	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2310859	0.81[ASN][1000 genomes]
rs2311491	0.82[ASN][1000 genomes]
rs2555702	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2555707	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2871615	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35140461	0.87[ASN][1000 genomes]
rs3755764	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755765	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773835	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773837	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3773838	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4380393	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4524250	0.88[ASN][1000 genomes]
rs4528914	0.82[ASN][1000 genomes]
rs4538351	0.83[ASN][1000 genomes]
rs57151068	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57526660	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57799705	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59128309	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59221985	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61052022	0.85[EUR][1000 genomes]
rs61151473	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61629363	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61708145	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439962	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439964	0.84[ASN][1000 genomes]
rs6764740	0.82[ASN][1000 genomes]
rs6770562	0.83[ASN][1000 genomes]
rs6772634	0.84[ASN][1000 genomes]
rs6773249	0.84[ASN][1000 genomes]
rs6785007	0.87[ASN][1000 genomes]
rs6785892	0.84[ASN][1000 genomes]
rs6788711	0.84[ASN][1000 genomes]
rs6789045	0.81[ASN][1000 genomes]
rs6789116	0.82[ASN][1000 genomes]
rs6797079	0.84[ASN][1000 genomes]
rs6810200	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs713354	0.81[JPT][hapmap]
rs72991025	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72991046	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621150	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7626525	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7632043	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7637899	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7638206	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7643287	0.94[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7643434	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7643614	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7644725	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7649116	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7652381	0.81[JPT][hapmap]
rs7653157	0.87[TSI][hapmap]
rs765990	0.84[ASN][1000 genomes]
rs877142	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs957093	0.82[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	nsv591865	chr3:140396022-140728850	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1005522	chr3:140454632-140685915	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536732	chr3:140454632-140685915	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv521218	chr3:140643038-140665147	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3364537	chr3:140646303-140668571	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11720342	SLC25A36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140646800-140650200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:140647000-140650000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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