Variant report

Variant	rs74089512
Chromosome Location	chr12:49849865-49849866
allele	G/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	chr12:49849836-49849889	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49761212..49762791-chr12:49849784..49851580,2	K562	blood:
2	chr12:49849137..49852050-chr12:49855425..49857339,2	K562	blood:
3	chr12:49848778..49850506-chr12:49860087..49862651,2	MCF-7	breast:

Variant related genes	Relation type
SPATS2	TF binding region
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11169014	0.81[ASN][1000 genomes]
rs4993294	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56322609	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57202083	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59689618	0.82[ASN][1000 genomes]
rs60418472	1.00[AFR][1000 genomes]
rs61375453	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6580715	0.81[ASN][1000 genomes]
rs7133398	0.81[ASN][1000 genomes]
rs74089508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089515	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089517	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74089520	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[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	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
2	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49798400-49856000	Weak transcription	Primary T cells from cord blood	blood
2	chr12:49820400-49854400	Weak transcription	Dnd41	blood
3	chr12:49823000-49854200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:49823000-49856000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
6	chr12:49823200-49856000	Weak transcription	NHEK	skin
7	chr12:49823200-49856400	Weak transcription	HSMM	muscle
8	chr12:49823400-49854400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:49823400-49856000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:49823400-49857400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:49823400-49876000	Weak transcription	Osteobl	bone
12	chr12:49828000-49863400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:49829400-49855000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:49831600-49852000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:49833600-49854600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr12:49837600-49856000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:49839200-49876000	Weak transcription	Fetal Thymus	thymus
18	chr12:49840200-49900600	Weak transcription	Pancreas	Pancrea
19	chr12:49840600-49856000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:49840600-49875800	Weak transcription	Hela-S3	cervix
21	chr12:49840800-49856000	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:49841800-49855800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:49843400-49856000	Weak transcription	Fetal Stomach	stomach
24	chr12:49845600-49856000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:49845800-49856800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:49846000-49879800	Weak transcription	Fetal Lung	lung
27	chr12:49846200-49855000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:49846400-49854600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:49846400-49854600	Weak transcription	GM12878-XiMat	blood
30	chr12:49846400-49878400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr12:49846800-49856000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:49847000-49858200	Weak transcription	Fetal Brain Female	brain
33	chr12:49847400-49855000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:49848000-49856000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:49848200-49856000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:49848400-49856000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:49848600-49850000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:49848600-49850600	Enhancers	Fetal Heart	heart
39	chr12:49848800-49854400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:49849200-49850000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:49849200-49850200	Enhancers	Right Ventricle	heart
42	chr12:49849200-49850400	Enhancers	Fetal Intestine Large	intestine
43	chr12:49849200-49854400	Weak transcription	NH-A	brain
44	chr12:49849400-49850000	Enhancers	Left Ventricle	heart
45	chr12:49849400-49856000	Weak transcription	Ovary	ovary
46	chr12:49849400-49856000	Weak transcription	Psoas Muscle	Psoas
47	chr12:49849400-49875800	Weak transcription	HepG2	liver
48	chr12:49849600-49850000	Enhancers	Gastric	stomach
49	chr12:49849600-49850000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr12:49849600-49850200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links