Variant report

Variant	rs1998699
Chromosome Location	chr6:55996417-55996418
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	FOXA1	chr6:55996344-55996511	ECC-1	luminal epithelium:	n/a	chr6:55996424-55996436

Variant related genes	Relation type
COL21A1	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1011277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1016719	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs11970688	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12198041	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1474698	0.85[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1925145	0.82[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1925152	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs1925165	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs1925166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925170	0.96[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes]
rs1925174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998700	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2076473	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2223598	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs2235735	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs2397203	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3823468	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs3846919	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes]
rs3899394	0.84[ASN][1000 genomes]
rs4310058	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs4374814	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4452633	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4612164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4712120	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs4715577	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs4715578	0.81[EUR][1000 genomes]
rs4715580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715583	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715584	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715590	0.84[ASN][1000 genomes]
rs4715594	0.82[CEU][hapmap]
rs6459130	0.86[ASN][1000 genomes]
rs6920461	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6926301	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6927562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6936386	0.86[ASN][1000 genomes]
rs761104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs761105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs764517	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7741903	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs7776118	0.82[CEU][hapmap];0.93[JPT][hapmap]
rs926534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs926535	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9296827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9296831	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs9296832	0.85[CEU][hapmap]
rs9296833	0.82[CEU][hapmap]
rs9349804	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs9357887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9357893	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9367676	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9370479	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs9370482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9382584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9396172	0.81[ASN][1000 genomes]
rs9396173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9396175	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs9475556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9475558	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs9475564	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9475565	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9475583	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475586	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475641	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55920600-56018400	Weak transcription	Ovary	ovary
2	chr6:55967800-56008600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:55979200-55998400	Weak transcription	Aorta	Aorta
4	chr6:55979200-55998400	Weak transcription	Fetal Stomach	stomach
5	chr6:55984000-56037000	Weak transcription	Fetal Kidney	kidney
6	chr6:55990400-56000800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:55993400-55998400	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:55993600-55998400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:55994400-55998800	Weak transcription	Fetal Lung	lung
10	chr6:55996200-55996600	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr6:55996400-56002000	Weak transcription	Psoas Muscle	Psoas

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