Variant report

Variant	rs62049596
Chromosome Location	chr16:77247329-77247330
allele	A/G
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	chr16:77246630..77248536-chr16:77252040..77254720,2	K562	blood:
4	chr16:77223923..77226639-chr16:77244818..77248823,8	K562	blood:
5	chr16:77247036..77249452-chr16:77252040..77253583,2	K562	blood:

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

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10781982	0.85[ASN][1000 genomes]
rs11149970	0.95[ASN][1000 genomes]
rs11149972	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11149975	0.86[ASN][1000 genomes]
rs11639911	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11649440	0.90[ASN][1000 genomes]
rs12447059	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12448094	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12716823	0.95[ASN][1000 genomes]
rs2113282	0.95[ASN][1000 genomes]
rs2232504	0.94[ASN][1000 genomes]
rs2232509	0.94[ASN][1000 genomes]
rs2241415	0.95[ASN][1000 genomes]
rs2241416	0.95[ASN][1000 genomes]
rs2278045	0.94[ASN][1000 genomes]
rs34143201	0.91[ASN][1000 genomes]
rs35660173	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3743759	0.94[ASN][1000 genomes]
rs3743761	0.94[ASN][1000 genomes]
rs3743762	0.94[ASN][1000 genomes]
rs3760004	0.92[ASN][1000 genomes]
rs3760005	0.92[ASN][1000 genomes]
rs3760006	0.95[ASN][1000 genomes]
rs3760007	0.95[ASN][1000 genomes]
rs4887893	0.94[ASN][1000 genomes]
rs62049594	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6420403	0.90[ASN][1000 genomes]
rs6564404	0.90[ASN][1000 genomes]
rs6564405	0.95[ASN][1000 genomes]
rs6564406	0.95[ASN][1000 genomes]
rs6564407	0.95[ASN][1000 genomes]
rs6564408	0.95[ASN][1000 genomes]
rs6564414	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7185297	0.94[ASN][1000 genomes]
rs7185889	0.95[ASN][1000 genomes]
rs7194408	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7195255	0.95[ASN][1000 genomes]
rs7202265	0.95[ASN][1000 genomes]
rs7204238	0.95[ASN][1000 genomes]
rs7205119	0.95[ASN][1000 genomes]
rs8047912	0.90[ASN][1000 genomes]
rs8048285	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8052509	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8062063	0.90[ASN][1000 genomes]
rs9923489	0.90[ASN][1000 genomes]
rs9924160	0.94[ASN][1000 genomes]
rs9924694	0.92[ASN][1000 genomes]
rs9930201	0.90[ASN][1000 genomes]
rs9930541	0.95[ASN][1000 genomes]
rs9939130	0.90[ASN][1000 genomes]
rs9939212	0.90[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62049596	SYCE1L	cis	Artery Tibial	GTEx
rs62049596	ADAMTS18	cis	brain	BrainEAC
rs62049596	ADAMTS18	cis	intralobular white matter	BrainEAC

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77245600-77247400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr16:77245600-77247400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr16:77245800-77247400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr16:77245800-77247400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:77245800-77247400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr16:77245800-77247400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr16:77245800-77247400	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr16:77245800-77247400	Active TSS	Primary T cells from cord blood	blood
9	chr16:77245800-77247400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr16:77245800-77247400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr16:77245800-77247400	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr16:77245800-77247400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr16:77245800-77247800	Flanking Active TSS	Right Ventricle	heart
14	chr16:77246200-77247400	Bivalent/Poised TSS	Stomach Mucosa	stomach
15	chr16:77246600-77247800	Flanking Active TSS	NH-A	brain
16	chr16:77246800-77247400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr16:77246800-77247400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr16:77246800-77247400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr16:77246800-77247400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
20	chr16:77246800-77247600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr16:77246800-77247800	Flanking Active TSS	HMEC	breast
22	chr16:77247000-77247400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr16:77247000-77247400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr16:77247000-77247400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr16:77247000-77247400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
26	chr16:77247000-77247400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr16:77247000-77247400	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr16:77247000-77247400	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
29	chr16:77247000-77247400	Enhancers	Placenta	Placenta
30	chr16:77247000-77247400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
31	chr16:77247000-77247400	Flanking Active TSS	HUVEC	blood vessel
32	chr16:77247000-77247600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr16:77247000-77247600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr16:77247000-77247600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr16:77247000-77247600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr16:77247000-77247800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr16:77247000-77247800	Enhancers	Gastric	stomach
38	chr16:77247000-77247800	Enhancers	Lung	lung
39	chr16:77247000-77248200	Enhancers	Fetal Heart	heart
40	chr16:77247000-77248400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr16:77247000-77248400	Enhancers	Left Ventricle	heart
42	chr16:77247000-77248600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr16:77247000-77248600	Bivalent Enhancer	NHDF-Ad	bronchial
44	chr16:77247000-77248800	Enhancers	Spleen	Spleen
45	chr16:77247200-77247400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
46	chr16:77247200-77247400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr16:77247200-77247400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr16:77247200-77247400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr16:77247200-77247400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
50	chr16:77247200-77247400	Enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links