Variant report

Variant	rs4454990
Chromosome Location	chr16:81140155-81140156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81128119..81130536-chr16:81138830..81141315,2	K562	blood:
2	chr16:81131183..81132698-chr16:81137237..81140172,2	MCF-7	breast:
3	chr16:81113091..81115144-chr16:81137957..81140174,2	K562	blood:

Variant related genes	Relation type
ENSG00000140905	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1035541	0.89[EUR][1000 genomes]
rs10459871	0.89[CEU][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs10459872	0.89[CEU][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs1048194	0.85[TSI][hapmap]
rs1050364	0.94[EUR][1000 genomes]
rs10514512	0.89[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes]
rs10514513	0.89[CEU][hapmap];0.84[CHB][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs10514514	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs10514515	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs11150341	0.81[CHB][hapmap]
rs11537	0.89[CEU][hapmap];0.92[MEX][hapmap]
rs11866124	0.80[CEU][hapmap];0.85[TSI][hapmap]
rs12443549	0.89[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12444137	0.89[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs12444974	0.80[CEU][hapmap];0.85[TSI][hapmap]
rs12445303	0.89[CEU][hapmap];0.85[CHB][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs12448806	0.92[EUR][1000 genomes]
rs12598621	0.94[EUR][1000 genomes]
rs12927239	1.00[MEX][hapmap]
rs13185	0.80[CEU][hapmap];0.81[MEX][hapmap]
rs1410	0.89[EUR][1000 genomes]
rs1412	0.92[EUR][1000 genomes]
rs1414	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs1563072	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs1563075	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs1563077	0.94[EUR][1000 genomes]
rs16954572	0.89[CEU][hapmap];0.85[CHB][hapmap];0.94[EUR][1000 genomes]
rs16954582	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs1814543	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2123624	0.83[CHD][hapmap]
rs2257378	0.87[MEX][hapmap]
rs2278022	0.83[JPT][hapmap];0.93[MEX][hapmap];0.82[EUR][1000 genomes]
rs2278024	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs2278025	0.85[CEU][hapmap]
rs2287995	0.82[EUR][1000 genomes]
rs2316730	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[EUR][1000 genomes]
rs2316731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2317085	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2317086	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2317087	0.92[EUR][1000 genomes]
rs2549891	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs2549896	0.89[CEU][hapmap]
rs2602402	0.89[CEU][hapmap]
rs2602407	0.89[CEU][hapmap]
rs2602431	0.81[MEX][hapmap]
rs28391685	0.94[EUR][1000 genomes]
rs28613188	0.94[EUR][1000 genomes]
rs28672349	0.94[EUR][1000 genomes]
rs2970076	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs4306521	0.94[EUR][1000 genomes]
rs4324141	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs4324142	0.94[EUR][1000 genomes]
rs4324143	0.94[EUR][1000 genomes]
rs4888124	0.81[CHB][hapmap]
rs4889225	0.89[CEU][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs4889227	0.94[EUR][1000 genomes]
rs4889229	0.83[EUR][1000 genomes]
rs4889230	0.83[EUR][1000 genomes]
rs4889231	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4889233	0.80[CEU][hapmap]
rs4889235	0.81[EUR][1000 genomes]
rs55939311	0.95[EUR][1000 genomes]
rs56032321	0.94[EUR][1000 genomes]
rs56119129	0.94[EUR][1000 genomes]
rs56166222	0.95[EUR][1000 genomes]
rs56198248	0.87[EUR][1000 genomes]
rs56286107	0.86[EUR][1000 genomes]
rs56375210	0.82[EUR][1000 genomes]
rs56395947	0.94[EUR][1000 genomes]
rs57606521	0.86[EUR][1000 genomes]
rs58144189	0.85[EUR][1000 genomes]
rs59177227	0.94[EUR][1000 genomes]
rs59685942	0.94[EUR][1000 genomes]
rs60481447	0.91[ASN][1000 genomes]
rs61082942	0.94[EUR][1000 genomes]
rs6420421	0.80[CEU][hapmap];0.85[TSI][hapmap]
rs6564820	0.81[JPT][hapmap]
rs6564821	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs6564822	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs7185637	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7188508	0.94[EUR][1000 genomes]
rs7203546	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7204040	0.89[CEU][hapmap];0.85[CHB][hapmap];0.94[EUR][1000 genomes]
rs7206814	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs73597252	0.87[EUR][1000 genomes]
rs73597259	0.94[ASN][1000 genomes]
rs73597265	0.91[ASN][1000 genomes]
rs754429	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs8043855	0.89[CEU][hapmap]
rs8045357	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs804885	0.89[CEU][hapmap];0.93[MEX][hapmap]
rs804895	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs804897	0.89[EUR][1000 genomes]
rs804902	0.89[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs8049509	0.92[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.89[ASN][1000 genomes]
rs8050906	0.89[JPT][hapmap]
rs8052490	0.89[CEU][hapmap];0.85[CHB][hapmap];0.94[EUR][1000 genomes]
rs8053975	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs8056972	0.89[CEU][hapmap];0.85[CHB][hapmap];0.94[EUR][1000 genomes]
rs8059153	0.90[CHD][hapmap]
rs8059692	0.80[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs8059769	0.81[JPT][hapmap]
rs8062357	0.83[CHB][hapmap]
rs8177843	0.87[ASN][1000 genomes]
rs8177851	0.84[EUR][1000 genomes]
rs8177876	0.87[EUR][1000 genomes]
rs8177939	0.91[EUR][1000 genomes]
rs8177940	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[EUR][1000 genomes]
rs8177942	0.95[EUR][1000 genomes]
rs8177943	0.94[EUR][1000 genomes]
rs8177945	0.92[EUR][1000 genomes]
rs8177948	0.94[EUR][1000 genomes]
rs8177950	0.94[EUR][1000 genomes]
rs8177957	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs8177959	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs874437	0.87[EUR][1000 genomes]
rs935942	0.89[CEU][hapmap];0.93[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9923732	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes]
rs9925940	0.89[CEU][hapmap];0.85[CHB][hapmap];0.94[EUR][1000 genomes]
rs9925943	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs9926174	0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs9929586	0.89[CEU][hapmap];0.85[CHB][hapmap];0.94[EUR][1000 genomes]
rs9933184	0.89[CEU][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.94[EUR][1000 genomes]
rs9935436	0.92[ASN][1000 genomes]
rs9938965	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv2751615	chr16:81093099-81307599	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv530715	chr16:81117168-81252875	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv907005	chr16:81121353-81194912	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1067144	chr16:81129298-81181641	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1059006	chr16:81139073-81155094	Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1063460	chr16:81139073-81157385	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4454990	GCSH	cis	Muscle Skeletal	GTEx
rs4454990	BM039	cis	multi-tissue	Pritchard
rs4454990	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs4454990	C16orf46	Cis_1M	lymphoblastoid	RTeQTL
rs4454990	ATMIN	cis	Muscle Skeletal	GTEx
rs4454990	DC13	cis	multi-tissue	Pritchard
rs4454990	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs4454990	CENPN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81130000-81141200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:81130000-81187600	Weak transcription	Right Atrium	heart
3	chr16:81131000-81140400	Weak transcription	Adipose Nuclei	Adipose
4	chr16:81137400-81140200	Weak transcription	HepG2	liver
5	chr16:81139200-81142800	Enhancers	Placenta	Placenta

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