Variant report

Variant	rs16943274
Chromosome Location	chr16:75795026-75795027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:75792670..75795394-chr16:75798183..75799774,2	K562	blood:
2	chr16:75680073..75682848-chr16:75794110..75795747,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TERF2IP-1	chr16:75794731-75795749	XLOC_011790

Variant related genes	Relation type
ENSG00000166848	Chromatin interaction
ENSG00000065427	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1133766	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11640406	0.82[EUR][1000 genomes]
rs11640743	0.82[EUR][1000 genomes]
rs11641108	0.82[EUR][1000 genomes]
rs11646086	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11646574	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11648206	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11649504	0.82[EUR][1000 genomes]
rs11649505	0.82[EUR][1000 genomes]
rs11649571	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11860980	0.85[EUR][1000 genomes]
rs11862453	0.85[EUR][1000 genomes]
rs11864677	0.82[EUR][1000 genomes]
rs11866252	1.00[CEU][hapmap]
rs12325271	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16941008	1.00[CEU][hapmap]
rs16942022	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16942809	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16942870	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs16943285	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17676012	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1991052	0.87[EUR][1000 genomes]
rs2233805	1.00[CEU][hapmap]
rs2233810	0.85[AMR][1000 genomes]
rs35135836	0.82[EUR][1000 genomes]
rs56892159	0.81[EUR][1000 genomes]
rs60415088	0.81[EUR][1000 genomes]
rs60545422	0.81[EUR][1000 genomes]
rs6834	1.00[CEU][hapmap]
rs7186790	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7195089	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7203608	0.94[EUR][1000 genomes]
rs73613267	0.85[EUR][1000 genomes]
rs73613272	0.85[EUR][1000 genomes]
rs73615089	0.81[EUR][1000 genomes]
rs73615301	0.94[EUR][1000 genomes]
rs8051771	1.00[CEU][hapmap]
rs8053257	0.85[CEU][hapmap]
rs9989360	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	43 gene(s)	inside rSNPs	diseases
5	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv906930	chr16:75728261-75872464	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1064607	chr16:75787129-76449101	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1065794	chr16:75792288-76434118	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv542961	chr16:75792288-76434118	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16943274	TMEM170A	cis	lymphoblastoid	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75789200-75795400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr16:75790400-75798000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr16:75792600-75795200	Weak transcription	GM12878-XiMat	blood
4	chr16:75794600-75798000	Weak transcription	Brain Anterior Caudate	brain
5	chr16:75794800-75795200	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr16:75794800-75795200	Flanking Active TSS	K562	blood
7	chr16:75794800-75795400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr16:75794800-75795400	Enhancers	Primary B cells from peripheral blood	blood

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