Variant report

Variant	rs16828467
Chromosome Location	chr1:174080163-174080164
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173835673..173838237-chr1:174076539..174080354,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10127823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10494491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10912702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10912716	0.83[ASN][1000 genomes]
rs10912717	0.82[ASN][1000 genomes]
rs10912721	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12029025	0.84[ASN][1000 genomes]
rs12058585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12060331	0.82[ASN][1000 genomes]
rs12060401	0.82[ASN][1000 genomes]
rs12067580	1.00[CEU][hapmap]
rs12071784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12072602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12072905	1.00[CEU][hapmap]
rs12077782	0.81[EUR][1000 genomes]
rs12077812	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12086826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12089005	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12089405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12093885	0.83[ASN][1000 genomes]
rs12562344	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12562588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12562959	0.84[EUR][1000 genomes]
rs12564848	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12564858	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12565675	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12565973	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12566022	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs12566122	0.88[JPT][hapmap]
rs12566642	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12566643	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs12566651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12566842	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12567854	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12567864	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12568869	1.00[AFR][1000 genomes]
rs12737218	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1321637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13375205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1407126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1407596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1407597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16846641	0.83[ASN][1000 genomes]
rs16846667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16846688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890881	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs1987873	0.82[ASN][1000 genomes]
rs2009083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2015075	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2025241	0.84[EUR][1000 genomes]
rs2227588	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs28595073	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2860841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2860845	0.82[EUR][1000 genomes]
rs2901784	0.83[ASN][1000 genomes]
rs36013663	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3980286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs41265242	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs41266044	0.92[EUR][1000 genomes]
rs4140468	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4536054	0.83[ASN][1000 genomes]
rs56926540	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57651489	0.85[EUR][1000 genomes]
rs58866024	0.87[EUR][1000 genomes]
rs59960208	0.84[ASN][1000 genomes]
rs60005461	0.87[EUR][1000 genomes]
rs60039606	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60551050	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826771	0.84[EUR][1000 genomes]
rs61826774	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826777	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61826779	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61826780	0.83[EUR][1000 genomes]
rs61826784	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61826785	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61826823	0.82[ASN][1000 genomes]
rs61826824	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61826826	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61826829	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61826831	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61827889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61827900	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61827901	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61827902	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61827903	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61827904	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61827905	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61828571	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61828574	0.90[EUR][1000 genomes]
rs61828575	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828576	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828577	0.92[EUR][1000 genomes]
rs61828578	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828580	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828583	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828584	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828587	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828589	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828590	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828591	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828592	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs61828595	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828622	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61828624	0.85[EUR][1000 genomes]
rs61828625	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61828627	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs61828630	1.00[AFR][1000 genomes]
rs61828631	1.00[AFR][1000 genomes]
rs61828635	1.00[AFR][1000 genomes]
rs61828895	0.84[EUR][1000 genomes]
rs61828898	0.84[EUR][1000 genomes]
rs61828899	0.84[EUR][1000 genomes]
rs6425262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6425264	0.81[ASN][1000 genomes]
rs6425267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6425271	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425272	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6657380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6661182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6665880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6668543	0.84[ASN][1000 genomes]
rs6676307	0.81[ASN][1000 genomes]
rs6680088	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6683276	0.82[ASN][1000 genomes]
rs6684527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6688176	0.82[ASN][1000 genomes]
rs6695887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6698123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6702454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6703547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs724416	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7523504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7525325	0.85[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes]
rs7528380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7547880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7549291	0.83[ASN][1000 genomes]
rs767053	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9425773	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9425775	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9425779	0.84[EUR][1000 genomes]
rs9425780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs961148	0.83[ASN][1000 genomes]
rs965498	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9728376	0.82[EUR][1000 genomes];0.81[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	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16828467	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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