Variant report

Variant	rs7741998
Chromosome Location	chr6:143982187-143982188
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	chr6:143979031..143980675-chr6:143980783..143983550,2	MCF-7	breast:
2	chr6:143980697..143982336-chr6:143982449..143985397,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11155318	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11155320	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11962519	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12530310	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13190772	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13191259	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs13204954	0.96[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13220613	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs2024693	0.80[AMR][1000 genomes]
rs2092762	0.96[EUR][1000 genomes]
rs3924968	0.83[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4299843	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4523103	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs6570571	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6570572	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs6570573	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs6913687	0.96[EUR][1000 genomes]
rs6914940	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6916245	0.85[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6931556	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7450663	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7738179	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs7741628	1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7741901	0.96[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7747182	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7758298	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7760178	0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7762598	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7764549	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7766091	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7770812	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7771214	0.96[CEU][hapmap]
rs7772898	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs7773502	1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs910419	0.96[CEU][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9321933	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs9321934	0.84[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9376773	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs9376774	0.90[MEX][hapmap];0.88[EUR][1000 genomes]
rs9376775	0.88[EUR][1000 genomes]
rs9376777	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9390127	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9399454	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9399456	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9403520	0.84[CEU][hapmap];0.99[EUR][1000 genomes]
rs9403522	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9484794	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs9496718	0.92[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs9496721	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs9496729	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9496733	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs9496734	0.83[EUR][1000 genomes]
rs9496735	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1032369	chr6:143925374-144007513	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv604805	chr6:143930404-144005949	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7741998	STX11	cis	parietal	SCAN
rs7741998	AIG1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143974600-143984400	Weak transcription	Fetal Intestine Large	intestine
2	chr6:143978000-143982200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:143980800-143983200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:143980800-143994200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:143981800-143994200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:143982000-143982200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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