Variant report

Variant	rs10424840
Chromosome Location	chr19:56827751-56827752
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 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	POLR2A	chr19:56827733-56827757	HepG2	liver:	n/a	n/a

No data

(count:10 , 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	chr19:56825335..56828118-chr19:56903219..56905060,3	K562	blood:
5	chr19:56165049..56166864-chr19:56826052..56827910,2	K562	blood:
6	chr19:56824639..56829612-chr19:56829732..56835885,11	K562	blood:
7	chr19:56825234..56827754-chr19:56833575..56835953,2	MCF-7	breast:
8	chr19:56152176..56154153-chr19:56826714..56828246,2	MCF-7	breast:
9	chr19:56806540..56808650-chr19:56825989..56828485,3	MCF-7	breast:
10	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
ENSG00000267298	TF binding region
ZSCAN5A	TF binding region
ENSG00000171425	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000018869	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000267454	Chromatin interaction
ENSG00000267710	Chromatin interaction
ENSG00000266907	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000240225	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10404293	0.87[CHB][hapmap]
rs10418888	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs11084444	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs11084445	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11878278	0.84[ASN][1000 genomes]
rs11882259	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2304122	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2869159	0.83[CHB][hapmap]
rs4801312	0.88[CHB][hapmap]
rs7252603	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8107755	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[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	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:43 , 50 per page) page: 1

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	chr19:56826800-56827800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr19:56827000-56827800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:56827200-56827800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:56827200-56827800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr19:56827200-56827800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
8	chr19:56827200-56827800	Enhancers	Fetal Heart	heart
9	chr19:56827200-56829400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr19:56827200-56829800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:56827200-56832200	Weak transcription	Placenta	Placenta
12	chr19:56827200-56832400	Weak transcription	Lung	lung
13	chr19:56827200-56832600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:56827400-56827800	Enhancers	Primary B cells from cord blood	blood
15	chr19:56827400-56827800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr19:56827400-56827800	Enhancers	Brain Angular Gyrus	brain
17	chr19:56827400-56827800	Enhancers	Brain Substantia Nigra	brain
18	chr19:56827400-56827800	Enhancers	Fetal Brain Male	brain
19	chr19:56827400-56827800	Enhancers	Left Ventricle	heart
20	chr19:56827400-56829600	Weak transcription	HSMMtube	muscle
21	chr19:56827400-56831000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr19:56827400-56831000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr19:56827400-56832400	Weak transcription	Right Ventricle	heart
24	chr19:56827600-56827800	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr19:56827600-56827800	Active TSS	Brain Hippocampus Middle	brain
26	chr19:56827600-56827800	Enhancers	Dnd41	blood
27	chr19:56827600-56828000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr19:56827600-56828400	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr19:56827600-56828400	Enhancers	Liver	Liver
30	chr19:56827600-56828800	Weak transcription	Pancreas	Pancrea
31	chr19:56827600-56828800	Weak transcription	HMEC	breast
32	chr19:56827600-56829200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:56827600-56829200	Enhancers	K562	blood
34	chr19:56827600-56829600	Enhancers	HepG2	liver
35	chr19:56827600-56829800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:56827600-56829800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:56827600-56829800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:56827600-56830200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:56827600-56830800	Weak transcription	Colonic Mucosa	Colon
40	chr19:56827600-56832200	Weak transcription	Right Atrium	heart
41	chr19:56827600-56832800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr19:56827600-56832800	Weak transcription	Fetal Kidney	kidney
43	chr19:56827600-56835400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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