Variant report

Variant	rs1019565
Chromosome Location	chr16:77229759-77229760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:77228836-77230139	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:77229570-77229771	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:77229694-77230092	K562	blood:	n/a	n/a
4	POLR2A	chr16:77229048-77229931	GM12878	blood:	n/a	n/a
5	POLR2A	chr16:77222637-77230176	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:77223534..77226455-chr16:77227601..77231752,9	MCF-7	breast:
2	chr16:77228552..77231268-chr16:77235268..77236824,2	MCF-7	breast:

Variant related genes	Relation type
SYCE1L	TF binding region
ENSG00000103111	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11149971	1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11544783	1.00[ASN][1000 genomes]
rs11860898	0.91[ASN][1000 genomes]
rs11863718	1.00[ASN][1000 genomes]
rs12931673	0.90[ASN][1000 genomes]
rs13329731	0.90[ASN][1000 genomes]
rs13329816	0.90[ASN][1000 genomes]
rs13330279	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330367	0.90[ASN][1000 genomes]
rs13332812	0.90[ASN][1000 genomes]
rs13336198	1.00[ASN][1000 genomes]
rs13337994	0.90[ASN][1000 genomes]
rs13339324	0.81[ASN][1000 genomes]
rs1428838	0.90[ASN][1000 genomes]
rs1428839	0.90[ASN][1000 genomes]
rs2017197	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232500	1.00[JPT][hapmap]
rs2232503	1.00[JPT][hapmap]
rs28539358	0.90[ASN][1000 genomes]
rs61746433	1.00[ASN][1000 genomes]
rs6564417	0.90[ASN][1000 genomes]
rs7184776	0.91[ASN][1000 genomes]
rs7188241	0.90[ASN][1000 genomes]
rs719053	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7198006	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7198588	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7201284	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7203467	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73627401	0.90[ASN][1000 genomes]
rs73633620	0.90[ASN][1000 genomes]
rs73633624	0.90[ASN][1000 genomes]
rs73633633	0.90[ASN][1000 genomes]
rs73633644	0.90[ASN][1000 genomes]
rs73633647	0.90[ASN][1000 genomes]
rs73633654	0.90[ASN][1000 genomes]
rs73633661	0.90[ASN][1000 genomes]
rs7501191	0.90[ASN][1000 genomes]
rs8048478	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9924958	1.00[ASN][1000 genomes]
rs9929722	0.90[ASN][1000 genomes]
rs9931082	1.00[ASN][1000 genomes]
rs9931400	0.90[ASN][1000 genomes]
rs9935921	0.90[ASN][1000 genomes]
rs9936182	0.90[ASN][1000 genomes]
rs9937408	0.90[ASN][1000 genomes]
rs9937693	0.90[ASN][1000 genomes]
rs9938871	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	nsv869201	chr16:76714549-77233646	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1057677	chr16:76861946-77230013	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77226200-77233000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:77226200-77240400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr16:77226400-77240200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr16:77226600-77233800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:77226600-77233800	Strong transcription	A549	lung
6	chr16:77226600-77234200	Strong transcription	Fetal Muscle Leg	muscle
7	chr16:77226600-77235000	Weak transcription	Psoas Muscle	Psoas
8	chr16:77226600-77235600	Strong transcription	Fetal Thymus	thymus
9	chr16:77226800-77230000	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr16:77226800-77233400	Strong transcription	NHLF	lung
11	chr16:77226800-77233800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr16:77226800-77233800	Strong transcription	Colonic Mucosa	Colon
13	chr16:77226800-77233800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr16:77226800-77234000	Strong transcription	Thymus	Thymus
15	chr16:77226800-77234000	Strong transcription	K562	blood
16	chr16:77226800-77234600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr16:77226800-77235200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:77226800-77235600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr16:77226800-77235600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr16:77226800-77235600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr16:77227000-77229800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr16:77227000-77230000	Strong transcription	Primary hematopoietic stem cells	blood
23	chr16:77227000-77230200	Strong transcription	Brain Hippocampus Middle	brain
24	chr16:77227000-77231200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr16:77227000-77232400	Weak transcription	Stomach Mucosa	stomach
26	chr16:77227000-77233800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr16:77227000-77233800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr16:77227000-77234000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr16:77227000-77234000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr16:77227000-77235600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr16:77227000-77235600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr16:77227000-77235600	Strong transcription	Liver	Liver
33	chr16:77227000-77235800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr16:77227000-77236200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr16:77227000-77236600	Strong transcription	Primary T cells from cord blood	blood
36	chr16:77227000-77246000	Weak transcription	Fetal Heart	heart
37	chr16:77227200-77230000	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr16:77227200-77230400	Strong transcription	Fetal Brain Female	brain
39	chr16:77227200-77230400	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr16:77227200-77233400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr16:77227200-77233400	Strong transcription	Brain Substantia Nigra	brain
42	chr16:77227200-77233800	Strong transcription	Rectal Smooth Muscle	rectum
43	chr16:77227200-77234000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr16:77227200-77234000	Strong transcription	Fetal Intestine Small	intestine
45	chr16:77227200-77234000	Strong transcription	Left Ventricle	heart
46	chr16:77227200-77234200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr16:77227200-77234600	Strong transcription	Fetal Stomach	stomach
48	chr16:77227200-77235600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr16:77227200-77235600	Strong transcription	Placenta	Placenta
50	chr16:77227200-77245800	Weak transcription	Fetal Kidney	kidney

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