Variant report

Variant	rs12052092
Chromosome Location	chr19:41318899-41318900
allele	A/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	POLR2A	chr19:41318705-41318951	K562	blood:	n/a	n/a
2	POLR2A	chr19:41318805-41319116	HUVEC	blood vessel:	n/a	n/a
3	NR3C1	chr19:41318640-41319423	A549	lung:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
4	NR3C1	chr19:41318621-41319426	A549	lung:	n/a	chr19:41319226-41319247 chr19:41319229-41319243 chr19:41319262-41319275 chr19:41319229-41319243
5	POLR2A	chr19:41318760-41319307	K562	blood:	n/a	n/a
6	POLR2A	chr19:41318656-41319149	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr19:41318830-41319108	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41312625..41314191-chr19:41317244..41319686,2	MCF-7	breast:
2	chr19:41307688..41310230-chr19:41318329..41321323,2	MCF-7	breast:
3	chr19:41304267..41305951-chr19:41317494..41319797,2	MCF-7	breast:

Variant related genes	Relation type
CYP2T2P	TF binding region
ENSG00000269858	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11547373	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35061187	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35405967	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733829	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3736329	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776611	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41530251	0.85[ASN][1000 genomes]
rs4802090	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802091	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803369	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73048928	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv521459	chr19:41313202-41333284	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41315000-41324400	Weak transcription	HepG2	liver
2	chr19:41315000-41332600	Weak transcription	Aorta	Aorta
3	chr19:41316000-41319400	Enhancers	Spleen	Spleen
4	chr19:41316000-41319800	Enhancers	Fetal Heart	heart
5	chr19:41316200-41324400	Weak transcription	Gastric	stomach
6	chr19:41316400-41325400	Weak transcription	Dnd41	blood
7	chr19:41317200-41319200	Enhancers	Lung	lung
8	chr19:41317200-41320800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr19:41317400-41319800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:41317400-41320200	Enhancers	Placenta	Placenta
11	chr19:41317400-41320400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr19:41317600-41320400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:41317600-41324000	Weak transcription	Hela-S3	cervix
14	chr19:41317600-41324400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:41317800-41319200	Enhancers	Adipose Nuclei	Adipose
16	chr19:41317800-41319400	Enhancers	Colonic Mucosa	Colon
17	chr19:41317800-41320000	Enhancers	Brain Substantia Nigra	brain
18	chr19:41317800-41324200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:41317800-41324400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:41317800-41324400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr19:41318000-41319000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:41318000-41319000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:41318000-41319000	Weak transcription	Left Ventricle	heart
24	chr19:41318000-41319000	Weak transcription	Right Ventricle	heart
25	chr19:41318000-41319200	Enhancers	Duodenum Mucosa	Duodenum
26	chr19:41318000-41319400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:41318000-41324400	Weak transcription	Pancreas	Pancrea
28	chr19:41318000-41324400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr19:41318000-41324400	Weak transcription	Right Atrium	heart
30	chr19:41318200-41319000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
31	chr19:41318200-41319200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:41318200-41319200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr19:41318200-41319200	Enhancers	Brain Anterior Caudate	brain
34	chr19:41318200-41319400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:41318200-41319400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:41318200-41319800	Enhancers	Colon Smooth Muscle	Colon
37	chr19:41318200-41319800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr19:41318200-41319800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr19:41318200-41319800	Enhancers	Ovary	ovary
40	chr19:41318200-41320000	Enhancers	Fetal Kidney	kidney
41	chr19:41318200-41320000	Enhancers	Rectal Smooth Muscle	rectum
42	chr19:41318200-41320200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr19:41318200-41320200	Weak transcription	A549	lung
44	chr19:41318200-41320400	Enhancers	Fetal Stomach	stomach
45	chr19:41318200-41323600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:41318200-41323800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:41318200-41324400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:41318400-41319000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
49	chr19:41318400-41319000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr19:41318400-41319000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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