Variant report

Variant	rs4808860
Chromosome Location	chr19:18954965-18954966
allele	A/C
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:7)
LncRNA
region (count:0)
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	IKZF1	chr19:18954814-18955096	GM12878	blood:	n/a	n/a
2	RUNX3	chr19:18953829-18955107	GM12878	blood:	n/a	n/a
3	RUNX3	chr19:18954708-18955137	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18948748..18952215-chr19:18952430..18955166,3	MCF-7	breast:
2	chr19:18951282..18956553-chr19:18964645..18969902,6	K562	blood:
3	chr19:18954859..18958448-chr19:18959389..18963601,5	MCF-7	breast:
4	chr19:18953438..18955479-chr19:18971688..18973215,2	MCF-7	breast:
5	chr19:18625178..18627279-chr19:18954295..18956518,2	K562	blood:
6	chr19:18900192..18902235-chr19:18954832..18957574,2	K562	blood:
7	chr19:18954190..18955830-chr19:18956609..18958808,3	MCF-7	breast:

No data

Variant related genes	Relation type
UPF1	TF binding region
ENSG00000005007	Chromatin interaction
ENSG00000105664	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10420509	1.00[LWK][hapmap]
rs1044823	1.00[LWK][hapmap]
rs11883356	1.00[TSI][hapmap]
rs4808874	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv911299	chr19:18939954-18984843	Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18945200-18956600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:18945800-18955000	Genic enhancers	Fetal Intestine Small	intestine
3	chr19:18946200-18958200	Weak transcription	Fetal Kidney	kidney
4	chr19:18947200-18958400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr19:18948600-18957200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr19:18948800-18955800	Enhancers	Right Ventricle	heart
7	chr19:18948800-18956400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:18948800-18957800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:18948800-18958400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:18948800-18959000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:18949000-18955200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr19:18949200-18955400	Enhancers	Liver	Liver
13	chr19:18949200-18956600	Enhancers	Left Ventricle	heart
14	chr19:18949200-18956800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr19:18949200-18958400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr19:18949800-18956800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr19:18949800-18958400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:18950000-18956200	Enhancers	Right Atrium	heart
19	chr19:18950000-18957800	Weak transcription	Primary B cells from cord blood	blood
20	chr19:18950200-18955200	Enhancers	Ovary	ovary
21	chr19:18950400-18955800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:18950600-18957800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:18950800-18956800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:18950800-18956800	Enhancers	Adipose Nuclei	Adipose
25	chr19:18950800-18958600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:18951000-18960800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:18951200-18956000	Weak transcription	NHEK	skin
28	chr19:18951200-18958400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:18951400-18955600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:18951400-18956600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:18951400-18956600	Enhancers	Fetal Muscle Trunk	muscle
32	chr19:18951400-18957800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr19:18951600-18955600	Enhancers	Pancreas	Pancrea
34	chr19:18951600-18956600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr19:18951600-18959000	Weak transcription	Psoas Muscle	Psoas
36	chr19:18951800-18956600	Weak transcription	Fetal Brain Female	brain
37	chr19:18951800-18958800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr19:18951800-18959200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:18951800-18977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr19:18952000-18955000	Enhancers	Stomach Smooth Muscle	stomach
41	chr19:18952000-18958000	Weak transcription	Fetal Brain Male	brain
42	chr19:18952000-18958600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr19:18952000-18961200	Weak transcription	Small Intestine	intestine
44	chr19:18952200-18955000	Enhancers	HepG2	liver
45	chr19:18952200-18955200	Enhancers	Primary B cells from peripheral blood	blood
46	chr19:18952200-18955800	Enhancers	Primary T cells fromperipheralblood	blood
47	chr19:18952200-18955800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr19:18952200-18956000	Weak transcription	Stomach Mucosa	stomach
49	chr19:18952200-18957200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:18952400-18956800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links