Variant report

Variant	rs57127559
Chromosome Location	chr16:46898486-46898487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:46898009..46901625-chr16:46916085..46918224,4	MCF-7	breast:
2	chr16:46897113..46899445-chr16:46917730..46919526,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166123	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1009391	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11860484	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861896	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862073	0.85[AFR][1000 genomes]
rs12934580	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12935606	0.90[EUR][1000 genomes]
rs1641122	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869006	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192644	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341043	1.00[ASN][1000 genomes]
rs35354454	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4246381	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966706	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966708	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966710	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966713	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967576	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967602	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967621	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006015	0.90[EUR][1000 genomes]
rs56042735	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56354199	0.89[EUR][1000 genomes]
rs57942848	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58074838	0.87[EUR][1000 genomes]
rs59708508	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62057633	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598777	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67211229	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67369452	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68162608	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7186748	0.90[EUR][1000 genomes]
rs7192574	0.85[EUR][1000 genomes]
rs7196375	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197485	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72812428	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8044443	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053137	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053297	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058734	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808432	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328668	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889198	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers 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	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1061651	chr16:46721805-46915511	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1060982	chr16:46721805-46938858	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	esv3519767	chr16:46873184-46960035	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3519768	chr16:46873184-46960035	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1795793	chr16:46882046-46904119	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57127559	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46886200-46905600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:46888400-46913400	Weak transcription	Esophagus	oesophagus
3	chr16:46890400-46902000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:46895200-46902400	Weak transcription	Fetal Intestine Large	intestine
5	chr16:46896600-46898800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr16:46896800-46898800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr16:46896800-46898800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr16:46896800-46899000	Enhancers	Stomach Mucosa	stomach
9	chr16:46897400-46898800	Flanking Active TSS	HepG2	liver
10	chr16:46897600-46898800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr16:46897600-46898800	Enhancers	Hela-S3	cervix
12	chr16:46897600-46898800	Enhancers	HMEC	breast
13	chr16:46897600-46899200	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr16:46897800-46900600	Enhancers	GM12878-XiMat	blood
15	chr16:46898000-46898600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr16:46898000-46898800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr16:46898000-46898800	Enhancers	NHEK	skin
18	chr16:46898000-46899200	Enhancers	Primary B cells from peripheral blood	blood
19	chr16:46898000-46899600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr16:46898000-46902400	Weak transcription	Liver	Liver
21	chr16:46898200-46898600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr16:46898200-46898600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr16:46898200-46898800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr16:46898200-46898800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr16:46898200-46898800	Enhancers	Placenta	Placenta
26	chr16:46898200-46898800	Enhancers	Pancreas	Pancrea
27	chr16:46898200-46898800	Enhancers	A549	lung
28	chr16:46898200-46899000	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr16:46898200-46899000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr16:46898200-46899400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr16:46898200-46901800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr16:46898400-46898800	Enhancers	HUVEC	blood vessel
33	chr16:46898400-46903600	Weak transcription	Rectal Mucosa Donor 29	rectum

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