Variant report

Variant	rs2278049
Chromosome Location	chr16:77246795-77246796
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:75678870..75681636-chr16:77246511..77249219,2	MCF-7	breast:
2	chr16:77224814..77227187-chr16:77245098..77247161,3	K562	blood:
3	chr16:77246630..77248536-chr16:77252040..77254720,2	K562	blood:
4	chr16:77223598..77226407-chr16:77245076..77246907,2	MCF-7	breast:
5	chr16:77223923..77226639-chr16:77244818..77248823,8	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MON1B-1	chr16:77246754-77246976	NONHSAT143795
2	lnc-MON1B-1	chr16:77246754-77247112	NONHSAT143798

No data

Variant related genes	Relation type
ENSG00000103111	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000226348	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs11865641	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12444706	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12444881	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12448895	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12599030	0.94[ASN][1000 genomes]
rs2161716	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232493	0.86[ASN][1000 genomes]
rs2278046	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278047	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278048	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2343035	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2343036	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887894	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4887896	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4888606	0.87[ASN][1000 genomes]
rs4888608	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56743953	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59418549	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61024035	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61032790	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61267588	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6564411	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7188097	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74027187	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74027188	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8055551	0.84[ASN][1000 genomes]
rs8061864	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8398	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9925950	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9928151	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9930815	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2278049	SYCE1L	cis	Nerve Tibial	GTEx
rs2278049	SYCE1L	cis	Stomach	GTEx
rs2278049	SYCE1L	cis	Artery Aorta	GTEx
rs2278049	SYCE1L	cis	Adipose Subcutaneous	GTEx
rs2278049	MON1B	Cis_1M	lymphoblastoid	RTeQTL
rs2278049	SYCE1L	cis	Artery Tibial	GTEx
rs2278049	SYCE1L	cis	Whole Blood	GTEx
rs2278049	SYCE1L	cis	Skin Sun Exposed Lower leg	GTEx
rs2278049	SYCE1L	cis	Thyroid	GTEx
rs2278049	SYCE1L	cis	Esophagus Mucosa	GTEx
rs2278049	SYCE1L	cis	lung	GTEx
rs2278049	RP11-538I12.2	cis	Esophagus Muscularis	GTEx
rs2278049	SYCE1L	cis	Muscle Skeletal	GTEx
rs2278049	SYCE1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77227200-77247200	Weak transcription	Hela-S3	cervix
2	chr16:77245400-77247200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr16:77245600-77246800	Flanking Bivalent TSS/Enh	HepG2	liver
4	chr16:77245600-77247200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr16:77245600-77247200	Active TSS	Brain Germinal Matrix	brain
6	chr16:77245600-77247400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr16:77245600-77247400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr16:77245800-77246800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr16:77245800-77247000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr16:77245800-77247000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:77245800-77247000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr16:77245800-77247000	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr16:77245800-77247000	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr16:77245800-77247000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr16:77245800-77247000	Bivalent/Poised TSS	Fetal Stomach	stomach
16	chr16:77245800-77247200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr16:77245800-77247200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr16:77245800-77247200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr16:77245800-77247200	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr16:77245800-77247200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr16:77245800-77247200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr16:77245800-77247200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr16:77245800-77247200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr16:77245800-77247200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr16:77245800-77247200	Active TSS	Brain Anterior Caudate	brain
26	chr16:77245800-77247200	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr16:77245800-77247200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
28	chr16:77245800-77247200	Active TSS	Fetal Brain Female	brain
29	chr16:77245800-77247200	Active TSS	Ovary	ovary
30	chr16:77245800-77247200	Active TSS	Psoas Muscle	Psoas
31	chr16:77245800-77247200	Active TSS	Rectal Smooth Muscle	rectum
32	chr16:77245800-77247200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
33	chr16:77245800-77247200	Active TSS	HSMM	muscle
34	chr16:77245800-77247200	Active TSS	NHEK	skin
35	chr16:77245800-77247400	Active TSS	H9 Cell Line	embryonic stem cell
36	chr16:77245800-77247400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr16:77245800-77247400	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr16:77245800-77247400	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr16:77245800-77247400	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr16:77245800-77247400	Active TSS	Primary T cells from cord blood	blood
41	chr16:77245800-77247400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr16:77245800-77247400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr16:77245800-77247400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr16:77245800-77247400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr16:77245800-77247800	Flanking Active TSS	Right Ventricle	heart
46	chr16:77246000-77246800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr16:77246000-77246800	Active TSS	Gastric	stomach
48	chr16:77246000-77246800	Active TSS	Spleen	Spleen
49	chr16:77246000-77247000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr16:77246000-77247000	Active TSS	Primary T cells fromperipheralblood	blood

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