Variant report

Variant	rs56743953
Chromosome Location	chr16:77248555-77248556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75678870..75681636-chr16:77246511..77249219,2	MCF-7	breast:
2	chr16:77240069..77243050-chr16:77247110..77249798,2	MCF-7	breast:
3	chr16:77223923..77226639-chr16:77244818..77248823,8	K562	blood:
4	chr16:77247036..77249452-chr16:77252040..77253583,2	K562	blood:

Variant related genes	Relation type
ENSG00000065427	Chromatin interaction
ENSG00000103111	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11865641	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12444706	0.89[ASN][1000 genomes]
rs12444881	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12448895	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12599030	0.94[ASN][1000 genomes]
rs2161716	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2232493	0.87[ASN][1000 genomes]
rs2278046	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278047	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278048	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278049	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2343035	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2343036	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887894	0.87[ASN][1000 genomes]
rs4887896	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888606	0.88[ASN][1000 genomes]
rs4888608	0.92[ASN][1000 genomes]
rs59418549	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61024035	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61032790	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61267588	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564411	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7188097	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74027187	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74027188	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8055551	0.84[ASN][1000 genomes]
rs8061864	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8398	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9925950	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9928151	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9930815	0.91[AMR][1000 genomes];0.88[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	nsv1065343	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv542965	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv1066258	chr16:77229953-77521919	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv542968	chr16:77229953-77521919	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs56743953	SYCE1L	cis	Artery Aorta	GTEx
rs56743953	MON1B	Cis_1M	lymphoblastoid	RTeQTL
rs56743953	SYCE1L	cis	Muscle Skeletal	GTEx
rs56743953	SYCE1L	cis	Nerve Tibial	GTEx
rs56743953	SYCE1L	cis	Adipose Subcutaneous	GTEx
rs56743953	SYCE1L	cis	Skin Sun Exposed Lower leg	GTEx
rs56743953	SYCE1L	cis	Esophagus Muscularis	GTEx
rs56743953	SYCE1L	cis	Thyroid	GTEx
rs56743953	SYCE1L	cis	lung	GTEx
rs56743953	SYCE1L	cis	Whole Blood	GTEx
rs56743953	SYCE1L	cis	Artery Tibial	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77247000-77248600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr16:77247000-77248600	Bivalent Enhancer	NHDF-Ad	bronchial
3	chr16:77247000-77248800	Enhancers	Spleen	Spleen
4	chr16:77247200-77248600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr16:77247200-77248600	Enhancers	NHLF	lung
6	chr16:77247200-77250200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:77247200-77253600	Weak transcription	Fetal Lung	lung
8	chr16:77247400-77248600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr16:77247400-77248800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr16:77247400-77248800	Enhancers	HUVEC	blood vessel
11	chr16:77247400-77254600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr16:77247600-77248600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr16:77247600-77248800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:77247600-77248800	Enhancers	Fetal Muscle Trunk	muscle
15	chr16:77247600-77251000	Weak transcription	Fetal Stomach	stomach
16	chr16:77247600-77254400	Weak transcription	Ovary	ovary
17	chr16:77247600-77257000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:77247800-77248600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr16:77247800-77248600	Weak transcription	Fetal Muscle Leg	muscle
20	chr16:77247800-77248600	Enhancers	NH-A	brain
21	chr16:77247800-77248800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr16:77247800-77248800	Enhancers	HMEC	breast
23	chr16:77247800-77250800	Weak transcription	HSMMtube	muscle
24	chr16:77247800-77253600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr16:77247800-77257400	Weak transcription	Esophagus	oesophagus
26	chr16:77247800-77261600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr16:77248200-77248600	Flanking Active TSS	A549	lung
28	chr16:77248400-77248800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:77248400-77248800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr16:77248400-77251200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr16:77248400-77253200	Weak transcription	Hela-S3	cervix
32	chr16:77248400-77256400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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