Variant report

Variant	rs7252523
Chromosome Location	chr19:18972591-18972592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18971903-18972601	GM12891	blood:	n/a	n/a
2	POLR2A	chr19:18972534-18973183	K562	blood:	n/a	n/a
3	POLR2A	chr19:18972190-18973234	K562	blood:	n/a	n/a
4	POLR2A	chr19:18971776-18972706	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:18971378-18973235	K562	blood:	n/a	n/a
6	POLR2A	chr19:18971795-18972900	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:18971926-18973035	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:18971538-18973237	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:18971880-18973023	GM12891	blood:	n/a	n/a
10	POLR2A	chr19:18972451-18972619	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr19:18972333-18973250	HL-60	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18970329..18972979-chr19:18987867..18989860,2	MCF-7	breast:
2	chr19:18970933..18973767-chr19:19052065..19053746,2	MCF-7	breast:
3	chr19:18953438..18955479-chr19:18971688..18973215,2	MCF-7	breast:
4	chr19:18971565..18973286-chr19:18974759..18978093,5	MCF-7	breast:
5	chr19:18914380..18916493-chr19:18970455..18972839,2	K562	blood:

No data

Variant related genes	Relation type
UPF1	TF binding region
ENSG00000051128	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10410987	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11673194	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2005695	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018392	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808161	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808163	0.93[EUR][1000 genomes]
rs4808164	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808859	0.85[ASN][1000 genomes]
rs4808866	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808868	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808869	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808870	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57870078	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7250661	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252796	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7257086	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73526907	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73526909	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757114	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886298	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv470132	chr19:18964442-19054720	Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 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	chr19:18951800-18977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:18953200-18977600	Weak transcription	Fetal Heart	heart
3	chr19:18954800-18979800	Strong transcription	Dnd41	blood
4	chr19:18956200-18978400	Strong transcription	Thymus	Thymus
5	chr19:18956800-18975200	Strong transcription	HepG2	liver
6	chr19:18958200-18977000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:18958400-18977600	Strong transcription	Fetal Intestine Large	intestine
8	chr19:18958400-18979000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:18958400-18979200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr19:18958400-18979400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:18958400-18979400	Strong transcription	Primary T cells from cord blood	blood
12	chr19:18958400-18979400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr19:18958400-18980200	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:18958600-18973200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
15	chr19:18958600-18976200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:18958600-18979000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:18958600-18979200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:18958600-18979400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:18958600-18979600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:18958800-18979200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr19:18958800-18979200	Strong transcription	Brain Germinal Matrix	brain
22	chr19:18959000-18979000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:18959000-18979000	Strong transcription	Gastric	stomach
24	chr19:18959200-18979200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:18959800-18978800	Strong transcription	Fetal Brain Female	brain
26	chr19:18960000-18979400	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr19:18960400-18977600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:18960400-18978600	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr19:18960400-18978800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:18960400-18979200	Strong transcription	Fetal Intestine Small	intestine
31	chr19:18960600-18977000	Strong transcription	Primary hematopoietic stem cells	blood
32	chr19:18960600-18979000	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr19:18960600-18979200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:18960600-18979400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr19:18960600-18979600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:18960600-18982600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:18960800-18973600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr19:18960800-18974800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr19:18960800-18975400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:18960800-18979200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:18960800-18979400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:18960800-18979400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:18961000-18979200	Strong transcription	Osteobl	bone
44	chr19:18961000-18979400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:18961000-18979600	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr19:18961000-18979600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:18961200-18979400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:18961200-18979400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:18961400-18979600	Strong transcription	Aorta	Aorta
50	chr19:18961600-18974600	Strong transcription	Pancreatic Islets	Pancreatic Islet

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