Variant report

Variant	rs73618201
Chromosome Location	chr19:56827505-56827506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr19:56824830-56827787	SK-N-SH	brain:	n/a	chr19:56826864-56826879 chr19:56826866-56826881 chr19:56826045-56826060 chr19:56826043-56826058
2	MXI1	chr19:56825144-56827667	IMR90	lung:	n/a	chr19:56826864-56826879 chr19:56826866-56826881 chr19:56826045-56826060 chr19:56826043-56826058
3	POLR2A	chr19:56827480-56827723	HepG2	liver:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56826282..56828501-chr19:56879622..56881209,2	K562	blood:
2	chr19:56825335..56828118-chr19:56903219..56906332,4	K562	blood:
3	chr19:56825352..56829856-chr19:56831358..56835885,6	K562	blood:
4	chr19:56651555..56653145-chr19:56824729..56827557,2	MCF-7	breast:
5	chr19:56631391..56633030-chr19:56824712..56827583,2	K562	blood:
6	chr19:56825335..56828118-chr19:56903219..56905060,3	K562	blood:
7	chr19:56631659..56633594-chr19:56825559..56827609,3	MCF-7	breast:
8	chr19:56165049..56166864-chr19:56826052..56827910,2	K562	blood:
9	chr19:56824639..56829612-chr19:56829732..56835885,11	K562	blood:
10	chr19:56612599..56616950-chr19:56825214..56827593,3	MCF-7	breast:
11	chr19:56825234..56827754-chr19:56833575..56835953,2	MCF-7	breast:
12	chr19:56152176..56154153-chr19:56826714..56828246,2	MCF-7	breast:
13	chr19:56806540..56808650-chr19:56825989..56828485,3	MCF-7	breast:
14	chr19:56654193..56655732-chr19:56826080..56828082,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF583-5	chr19:56826623-56828172	ENSG00000267549.1

No data

Variant related genes	Relation type
ZSCAN5A	TF binding region
ENSG00000267298	TF binding region
ENSG00000240225	Chromatin interaction
ENSG00000267710	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000267454	Chromatin interaction
ENSG00000018869	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000266907	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000223060	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs58997200	1.00[AMR][1000 genomes]
rs60628802	1.00[AMR][1000 genomes]
rs61079647	1.00[AMR][1000 genomes]
rs61389610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7247773	1.00[AMR][1000 genomes]
rs7257563	1.00[AMR][1000 genomes]
rs73618178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73618195	1.00[AMR][1000 genomes]
rs73621209	1.00[AMR][1000 genomes]
rs73626790	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73628710	1.00[AMR][1000 genomes]
rs73628723	1.00[AMR][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	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
4	nsv526325	chr19:56741186-56852035	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
7	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
9	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
10	nsv1058026	chr19:56799847-56833153	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv1067261	chr19:56820571-56854916	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56825000-56827800	Active TSS	A549	lung
2	chr19:56825200-56827800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:56825400-56827600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:56825400-56827600	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr19:56825400-56827600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:56825600-56827600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:56825600-56827600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr19:56825800-56827600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:56826600-56827600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr19:56826600-56827600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr19:56826800-56827600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:56826800-56827600	Flanking Active TSS	Liver	Liver
13	chr19:56826800-56827600	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr19:56826800-56827600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr19:56826800-56827600	Flanking Active TSS	Dnd41	blood
16	chr19:56826800-56827600	Flanking Active TSS	NHEK	skin
17	chr19:56826800-56827800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr19:56827000-56827600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:56827000-56827600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:56827000-56827600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:56827000-56827600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:56827000-56827600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:56827000-56827600	Enhancers	Spleen	Spleen
24	chr19:56827000-56827600	Flanking Active TSS	GM12878-XiMat	blood
25	chr19:56827000-56827600	Flanking Active TSS	Hela-S3	cervix
26	chr19:56827000-56827600	Flanking Active TSS	HepG2	liver
27	chr19:56827000-56827600	Flanking Active TSS	HMEC	breast
28	chr19:56827000-56827600	Flanking Active TSS	K562	blood
29	chr19:56827000-56827800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:56827200-56827600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:56827200-56827600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:56827200-56827600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:56827200-56827600	Enhancers	Primary B cells from peripheral blood	blood
34	chr19:56827200-56827600	Enhancers	Primary T cells from cord blood	blood
35	chr19:56827200-56827600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:56827200-56827600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr19:56827200-56827600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:56827200-56827600	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr19:56827200-56827600	Flanking Active TSS	Fetal Kidney	kidney
40	chr19:56827200-56827600	Enhancers	Fetal Lung	lung
41	chr19:56827200-56827600	Enhancers	Fetal Muscle Leg	muscle
42	chr19:56827200-56827600	Enhancers	Pancreas	Pancrea
43	chr19:56827200-56827800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:56827200-56827800	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr19:56827200-56827800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr19:56827200-56827800	Enhancers	Fetal Heart	heart
47	chr19:56827200-56829400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr19:56827200-56829800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr19:56827200-56832200	Weak transcription	Placenta	Placenta
50	chr19:56827200-56832400	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links