Variant report

Variant	rs2287995
Chromosome Location	chr16:81095099-81095100
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81093322..81097410-chr16:81102754..81106923,4	MCF-7	breast:
2	chr16:81093718..81096458-chr16:81477922..81479889,2	K562	blood:
3	chr16:81093754..81095861-chr16:81110102..81112383,2	MCF-7	breast:
4	chr16:81094141..81096818-chr16:81110183..81111758,2	K562	blood:

Variant related genes	Relation type
ENSG00000153815	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000261838	Chromatin interaction
ENSG00000245059	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1035541	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10459871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10459872	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048194	0.87[EUR][1000 genomes]
rs1050364	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10514512	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10514513	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514514	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10514515	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11150337	0.86[EUR][1000 genomes]
rs11150338	0.85[ASN][1000 genomes]
rs11537	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11863158	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11865207	0.84[EUR][1000 genomes]
rs12443549	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12444137	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12444747	0.87[EUR][1000 genomes]
rs12444969	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12445303	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12456	0.85[EUR][1000 genomes]
rs12598621	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12927239	0.82[EUR][1000 genomes]
rs12927828	0.84[EUR][1000 genomes]
rs1410	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1412	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1414	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1563075	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1563077	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16954513	0.81[EUR][1000 genomes]
rs16954572	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16954582	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2278022	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278024	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278025	0.86[EUR][1000 genomes]
rs2317085	0.82[EUR][1000 genomes]
rs2317086	0.81[EUR][1000 genomes]
rs2549891	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2549896	0.84[EUR][1000 genomes]
rs2602402	0.87[EUR][1000 genomes]
rs2602404	0.84[EUR][1000 genomes]
rs2602407	0.88[EUR][1000 genomes]
rs28391685	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28613188	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28672349	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2970076	0.84[EUR][1000 genomes]
rs35096487	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4306521	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4324141	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4324142	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4324143	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4454990	0.82[EUR][1000 genomes]
rs4889227	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4889231	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55939311	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56032321	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56119129	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56166222	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56395947	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58144189	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59177227	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59685942	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61082942	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62054594	0.92[ASN][1000 genomes]
rs7188508	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7204040	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs754429	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804885	0.88[EUR][1000 genomes]
rs804889	0.87[ASN][1000 genomes]
rs804895	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs804897	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8052490	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8056972	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8177939	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8177940	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8177942	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8177943	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8177945	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8177948	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8177950	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8177959	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9806918	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9923732	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925940	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925943	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9926174	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9929586	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9933184	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9938965	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][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	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	35 gene(s)	inside rSNPs	diseases
7	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
8	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1897	chr16:81060566-81105260	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	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
11	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2287995	C16orf46	Cis_1M	lymphoblastoid	RTeQTL
rs2287995	GCSH///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs2287995	GCSH///LOC654085///LOC730107	Cis_1M	lymphoblastoid	RTeQTL
rs2287995	ATMIN	cis	Muscle Skeletal	GTEx
rs2287995	CENPN	Cis_1M	lymphoblastoid	RTeQTL
rs2287995	GCSH	cis	Muscle Skeletal	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81079400-81109800	Weak transcription	Brain Hippocampus Middle	brain
2	chr16:81080400-81110200	Weak transcription	Ovary	ovary
3	chr16:81083800-81099800	Weak transcription	Brain Angular Gyrus	brain
4	chr16:81088800-81095400	Weak transcription	Fetal Stomach	stomach
5	chr16:81090200-81097600	Weak transcription	Pancreas	Pancrea
6	chr16:81092000-81106600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:81093000-81109800	Weak transcription	Brain Anterior Caudate	brain
8	chr16:81093200-81100200	Weak transcription	Brain Germinal Matrix	brain
9	chr16:81093600-81100000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr16:81094200-81095200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr16:81094200-81095600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr16:81094200-81095600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr16:81094200-81096000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr16:81094400-81095200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr16:81094400-81095200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr16:81094400-81095400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr16:81094400-81095400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr16:81094400-81095600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr16:81094400-81095600	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr16:81094400-81096200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr16:81094600-81098000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr16:81094800-81095200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr16:81094800-81095600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr16:81094800-81095600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr16:81095000-81095400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:81095000-81095600	Enhancers	Fetal Muscle Trunk	muscle
27	chr16:81095000-81109400	Weak transcription	H9 Cell Line	embryonic stem cell

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