Variant report

Variant	rs7252796
Chromosome Location	chr19:18990396-18990397
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	IRF1	chr19:18990310-18991210	K562	blood:	n/a	chr19:18990805-18990819 chr19:18990912-18990926 chr19:18990982-18990996 chr19:18991004-18991018
2	POLR2A	chr19:18988598-18991468	MCF-7	breast:	n/a	n/a
3	SP4	chr19:18990177-18991203	H1-hESC	embryonic stem cell:	n/a	chr19:18991006-18991022 chr19:18990805-18990821 chr19:18990984-18991000 chr19:18991004-18991020 chr19:18990982-18990998 chr19:18990912-18990928 chr19:18990807-18990818
4	EGR1	chr19:18990080-18991112	K562	blood:	n/a	chr19:18990987-18991000 chr19:18990985-18990995
5	POLR2A	chr19:18990196-18990428	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:18990386-18990552	ProgFib	skin:	n/a	n/a
7	POLR2A	chr19:18990074-18990571	K562	blood:	n/a	n/a
8	POLR2A	chr19:18990164-18990429	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:18988692-18991381	Hela-S3	cervix:	n/a	n/a
10	STAT3	chr19:18990359-18990915	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr19:18990166-18990414	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18867338..18869538-chr19:18987734..18990558,2	K562	blood:
2	chr19:18989707..18992076-chr19:19050980..19053421,2	K562	blood:
3	chr19:18965705..18968424-chr19:18988642..18991060,2	K562	blood:
4	chr19:18984024..18987729-chr19:18988322..18991283,4	K562	blood:
5	chr19:18989338..18991884-chr19:19005552..19007379,3	MCF-7	breast:
6	chr19:18941192..18944158-chr19:18989151..18991227,3	K562	blood:
7	chr19:18973585..18975733-chr19:18989912..18992220,3	K562	blood:

Variant related genes	Relation type
ENSG00000269694	TF binding region
ENSG00000130283	Chromatin interaction
ENSG00000051128	Chromatin interaction
ENSG00000005007	Chromatin interaction
ENSG00000223802	Chromatin interaction
ENSG00000269019	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10410987	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11673194	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2005695	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2018392	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808161	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4808164	0.85[ASN][1000 genomes]
rs4808866	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4808868	0.81[ASN][1000 genomes]
rs4808869	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4808870	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57870078	0.85[ASN][1000 genomes]
rs7250661	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7252523	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7257086	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73526907	0.86[ASN][1000 genomes]
rs73526909	0.87[ASN][1000 genomes]
rs757114	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs886298	0.89[AMR][1000 genomes];0.88[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	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
7	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
8	nsv828473	chr19:18975130-18994875	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18979600-18991800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr19:18980400-19004000	Weak transcription	Psoas Muscle	Psoas
3	chr19:18980400-19004200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr19:18980800-18990400	Weak transcription	Pancreas	Pancrea
5	chr19:18981400-18998000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:18981800-18997800	Weak transcription	Ovary	ovary
7	chr19:18981800-19005800	Weak transcription	Right Atrium	heart
8	chr19:18982000-18991400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr19:18982000-19002200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:18982400-18995200	Strong transcription	Brain Anterior Caudate	brain
11	chr19:18982600-19000800	Weak transcription	Colon Smooth Muscle	Colon
12	chr19:18983400-18998200	Strong transcription	Brain Cingulate Gyrus	brain
13	chr19:18984000-18995600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr19:18984000-19004200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:18984600-18995000	Strong transcription	Brain Hippocampus Middle	brain
16	chr19:18984800-18995200	Strong transcription	Brain Angular Gyrus	brain
17	chr19:18984800-18995200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:18985600-19004400	Weak transcription	Fetal Brain Male	brain
19	chr19:18986600-18995000	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr19:18987200-19004200	Weak transcription	HSMMtube	muscle
21	chr19:18987400-18991000	Weak transcription	Fetal Kidney	kidney
22	chr19:18987600-18990400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:18988000-18991000	Weak transcription	Hela-S3	cervix
24	chr19:18988000-18995200	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr19:18988000-19005400	Weak transcription	A549	lung
26	chr19:18988200-18990400	Strong transcription	Brain Substantia Nigra	brain
27	chr19:18988200-18993000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:18988200-18993800	Weak transcription	Aorta	Aorta
29	chr19:18988200-18994400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:18988200-18995600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:18988200-19004800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:18988400-18991000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:18988400-18992000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:18988400-18995200	Strong transcription	Brain Germinal Matrix	brain
35	chr19:18988400-18995200	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr19:18988400-18995200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr19:18988400-18996000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:18988400-18998400	Strong transcription	Fetal Muscle Leg	muscle
39	chr19:18988600-18991000	Weak transcription	Placenta	Placenta
40	chr19:18988800-18994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr19:18989000-18990600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:18989000-18991200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:18989000-18991200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr19:18989200-18999000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:18989200-18999200	Strong transcription	Fetal Brain Female	brain
46	chr19:18989400-18990400	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr19:18989400-18991200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:18989600-18991000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr19:18989600-18991000	Weak transcription	Colonic Mucosa	Colon
50	chr19:18989800-18991200	Weak transcription	Fetal Intestine Small	intestine

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