Variant report

Variant	rs11759727
Chromosome Location	chr6:88003299-88003300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TFAP2A	chr6:88003177-88003656	Hela-S3	cervix:	n/a	chr6:88003446-88003456 chr6:88003446-88003456 chr6:88003444-88003459 chr6:88003446-88003456 chr6:88003446-88003456
2	FOSL2	chr6:88003206-88003687	MCF-7	breast:	n/a	chr6:88003325-88003333
3	FOSL2	chr6:88003184-88003662	MCF-7	breast:	n/a	chr6:88003325-88003333
4	NR2F2	chr6:88003228-88003709	MCF-7	breast:	n/a	n/a
5	FOS	chr6:88003281-88003620	MCF10A-Er-Src	breast:	n/a	chr6:88003325-88003333
6	FOS	chr6:88003281-88003637	MCF10A-Er-Src	breast:	n/a	chr6:88003325-88003333
7	HDAC2	chr6:88003277-88003624	MCF-7	breast:	n/a	n/a
8	FOS	chr6:88003287-88003613	MCF10A-Er-Src	breast:	n/a	chr6:88003325-88003333
9	TCF7L2	chr6:88003241-88003595	Hela-S3	cervix:	n/a	n/a
10	TFAP2C	chr6:88003163-88003711	Hela-S3	cervix:	n/a	chr6:88003442-88003457
11	FOS	chr6:88003284-88003627	MCF10A-Er-Src	breast:	n/a	chr6:88003325-88003333
12	CEBPB	chr6:88003287-88003615	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:88003084..88004610-chr6:88029635..88031151,2	K562	blood:
2	chr6:88002598..88005293-chr6:88032419..88034382,2	MCF-7	breast:
3	chr6:88002030..88003549-chr6:88007137..88009504,2	MCF-7	breast:

Variant related genes	Relation type
GJB7	TF binding region
ENSG00000164411	Chromatin interaction
ENSG00000216990	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1145713	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1145714	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1145715	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1145716	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1188806	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1188816	0.85[ASN][1000 genomes]
rs1188817	0.84[ASN][1000 genomes]
rs1188818	0.84[ASN][1000 genomes]
rs1188819	0.86[ASN][1000 genomes]
rs1203162	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203163	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203164	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12194354	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12211627	0.85[ASN][1000 genomes]
rs13201289	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1630494	0.86[ASN][1000 genomes]
rs16878497	0.82[EUR][1000 genomes]
rs1739886	0.84[ASN][1000 genomes]
rs1746444	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1753152	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1753159	0.86[ASN][1000 genomes]
rs181491	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925686	0.83[EUR][1000 genomes]
rs2236048	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2257153	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs242264	0.86[ASN][1000 genomes]
rs242265	0.86[ASN][1000 genomes]
rs242266	0.86[ASN][1000 genomes]
rs242268	0.86[ASN][1000 genomes]
rs242269	0.86[ASN][1000 genomes]
rs242274	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs242275	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs242276	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs242277	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs242282	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983136	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs368267	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs374792	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs377288	0.82[ASN][1000 genomes]
rs379455	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs381741	0.86[ASN][1000 genomes]
rs381798	0.86[ASN][1000 genomes]
rs382956	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs383692	0.84[ASN][1000 genomes]
rs384318	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs385210	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3857486	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs392807	0.86[ASN][1000 genomes]
rs398140	0.85[ASN][1000 genomes]
rs3999791	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs406981	0.84[ASN][1000 genomes]
rs411606	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs413687	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs414453	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4235830	0.84[EUR][1000 genomes]
rs452315	0.86[ASN][1000 genomes]
rs4707344	0.83[EUR][1000 genomes]
rs4707345	0.84[EUR][1000 genomes]
rs4707355	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs490447	0.86[ASN][1000 genomes]
rs540975	0.86[ASN][1000 genomes]
rs541170	0.86[ASN][1000 genomes]
rs6908834	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6913159	0.84[EUR][1000 genomes]
rs6921673	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926686	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932641	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6938885	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939075	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940325	0.85[EUR][1000 genomes]
rs7752414	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7757330	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs827433	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs910564	0.86[ASN][1000 genomes]
rs910565	0.86[ASN][1000 genomes]
rs912815	0.83[EUR][1000 genomes]
rs9294375	0.81[EUR][1000 genomes]
rs9294376	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444476	0.81[EUR][1000 genomes]
rs9444481	0.84[EUR][1000 genomes]
rs9444486	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444488	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9444490	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444491	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450623	0.82[EUR][1000 genomes]
rs9450630	0.84[EUR][1000 genomes]
rs9450636	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450637	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450638	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450639	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450640	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450646	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450651	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450653	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11759727	C6orf162	cis	multi-tissue	Pritchard
rs11759727	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs11759727	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs11759727	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88000600-88004600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:88001200-88004200	Enhancers	Hela-S3	cervix
3	chr6:88003200-88003600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr6:88003200-88003800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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