Variant report

Variant	rs2231998
Chromosome Location	chr19:19032680-19032681
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:4)
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	chr19:19032093-19032717	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:19031832-19034016	U87	brain:	n/a	n/a
3	POLR2A	chr19:19032465-19032776	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr19:19032614-19032935	HCT-116	colon:	n/a	n/a
5	POLR2A	chr19:19031838-19033917	U87	brain:	n/a	n/a
6	POLR2A	chr19:19031933-19032694	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr19:19032510-19032744	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:19032610-19032708	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr19:19032092-19032955	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr19:19032361-19032717	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:19031896-19034067	HL-60	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19031206..19033838-chr19:19067854..19070474,2	MCF-7	breast:
2	chr19:19028307..19038067-chr19:19048419..19054729,15	MCF-7	breast:
3	chr19:19028142..19040542-chr19:19046967..19057144,34	MCF-7	breast:
4	chr19:19005129..19007826-chr19:19028734..19032982,4	MCF-7	breast:

No data

Variant related genes	Relation type
DDX49	TF binding region
COPE	TF binding region
ENSG00000241172	Chromatin interaction
ENSG00000051128	Chromatin interaction
ENSG00000269019	Chromatin interaction
ENSG00000130283	Chromatin interaction
ENSG00000223802	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10414989	1.00[EUR][1000 genomes]
rs11537890	1.00[EUR][1000 genomes]
rs11879043	1.00[TSI][hapmap]
rs2231987	1.00[EUR][1000 genomes]
rs55639837	1.00[EUR][1000 genomes]
rs55689008	1.00[EUR][1000 genomes]
rs56343246	1.00[EUR][1000 genomes]
rs57534766	1.00[EUR][1000 genomes]
rs58569954	1.00[EUR][1000 genomes]
rs59049077	1.00[EUR][1000 genomes]
rs73923181	1.00[EUR][1000 genomes]
rs73923182	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
4	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
5	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
6	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
7	nsv911301	chr19:18994638-19077385	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911302	chr19:18995201-19088981	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
10	nsv543926	chr19:19029529-19062771	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2231998	FOXG1	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19031400-19033000	Weak transcription	Aorta	Aorta
2	chr19:19031400-19033200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:19031400-19033200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:19031600-19032800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr19:19031600-19032800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr19:19031600-19032800	Genic enhancers	Fetal Muscle Trunk	muscle
7	chr19:19031600-19032800	Weak transcription	Left Ventricle	heart
8	chr19:19031600-19032800	Weak transcription	HSMMtube	muscle
9	chr19:19031600-19032800	Weak transcription	NHDF-Ad	bronchial
10	chr19:19031600-19033000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:19031600-19033200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:19031600-19033200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:19031600-19033200	Weak transcription	Brain Substantia Nigra	brain
14	chr19:19031600-19033400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:19031600-19033400	Weak transcription	Stomach Mucosa	stomach
16	chr19:19031600-19033600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:19031600-19033800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr19:19031600-19033800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr19:19031600-19034000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:19031600-19034400	Weak transcription	NH-A	brain
21	chr19:19031600-19034600	Strong transcription	K562	blood
22	chr19:19031600-19035000	Weak transcription	Psoas Muscle	Psoas
23	chr19:19031600-19035200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:19031600-19035400	Weak transcription	Fetal Kidney	kidney
25	chr19:19031600-19035400	Weak transcription	Small Intestine	intestine
26	chr19:19031600-19037400	Strong transcription	NHLF	lung
27	chr19:19031600-19042600	Weak transcription	Fetal Heart	heart
28	chr19:19031600-19042600	Strong transcription	Fetal Intestine Small	intestine
29	chr19:19031600-19043200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:19031600-19043200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr19:19031600-19043200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:19031600-19044000	Weak transcription	HSMM	muscle
33	chr19:19031600-19045200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:19031800-19032800	Weak transcription	A549	lung
35	chr19:19031800-19033000	Weak transcription	Primary B cells from cord blood	blood
36	chr19:19031800-19033000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr19:19031800-19033400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:19031800-19033600	Weak transcription	Hela-S3	cervix
39	chr19:19031800-19040600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:19031800-19042800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr19:19031800-19043400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr19:19031800-19043400	Strong transcription	Fetal Stomach	stomach
43	chr19:19032000-19033400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:19032000-19037200	Strong transcription	Esophagus	oesophagus
45	chr19:19032000-19039800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr19:19032000-19039800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:19032000-19040000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:19032000-19040400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:19032000-19040600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:19032000-19040600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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