Variant report

Variant	rs12423130
Chromosome Location	chr12:50643958-50643959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:50643642-50644005	K562	blood:	n/a	n/a
2	RUNX3	chr12:50643299-50644033	GM12878	blood:	n/a	n/a
3	EGR1	chr12:50643690-50643985	K562	blood:	n/a	n/a
4	RUNX3	chr12:50643570-50643973	GM12878	blood:	n/a	n/a
5	ESR1	chr12:50643474-50644085	ECC-1	luminal epithelium:	n/a	n/a
6	NR2F2	chr12:50643644-50644039	K562	blood:	n/a	n/a
7	ZNF384	chr12:50643685-50644567	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:50639732..50644182-chr12:50792343..50795361,4	K562	blood:
2	chr12:50614825..50617496-chr12:50643116..50645944,3	K562	blood:
3	chr12:50641106..50644296-chr12:50675797..50678807,3	K562	blood:
4	chr12:50643519..50647012-chr12:50649051..50651928,4	K562	blood:
5	chr12:50610860..50612440-chr12:50643733..50646467,2	MCF-7	breast:

No data

Variant related genes	Relation type
LIMA1	TF binding region
ENSG00000050405	Chromatin interaction
ENSG00000161813	Chromatin interaction
ENSG00000212496	Chromatin interaction
ENSG00000257531	Chromatin interaction
ENSG00000203433	Chromatin interaction

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

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

rs_ID	r²[population]
rs10450773	0.83[EUR][1000 genomes]
rs10747572	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783346	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783347	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28364704	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3815671	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61928280	0.89[EUR][1000 genomes]
rs7302422	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs736167	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7974834	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8181651	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
5	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50616800-50651800	Weak transcription	Brain Anterior Caudate	brain
2	chr12:50627600-50644600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr12:50633200-50651200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:50634600-50648200	Weak transcription	Spleen	Spleen
5	chr12:50635600-50646600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:50636200-50651200	Weak transcription	Fetal Kidney	kidney
7	chr12:50636600-50651400	Weak transcription	Gastric	stomach
8	chr12:50636600-50651800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:50636800-50648200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:50637200-50645600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:50637200-50648200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:50639000-50651600	Weak transcription	Fetal Lung	lung
13	chr12:50640000-50644000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:50640000-50644000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr12:50640000-50644200	Enhancers	Osteobl	bone
16	chr12:50640200-50644400	Genic enhancers	Fetal Intestine Small	intestine
17	chr12:50640400-50644000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:50640400-50651200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:50640600-50645400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:50640800-50647400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:50641000-50662000	Weak transcription	Brain Germinal Matrix	brain
22	chr12:50641200-50653200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:50641400-50647800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:50641400-50659600	Weak transcription	Esophagus	oesophagus
25	chr12:50641800-50648400	Weak transcription	Lung	lung
26	chr12:50641800-50651200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:50641800-50651200	Weak transcription	Left Ventricle	heart
28	chr12:50641800-50651200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:50641800-50651800	Weak transcription	Fetal Stomach	stomach
30	chr12:50641800-50651800	Weak transcription	Right Ventricle	heart
31	chr12:50641800-50652000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:50642000-50645600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:50642400-50644000	Enhancers	Hela-S3	cervix
34	chr12:50642600-50644000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:50642600-50644000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr12:50642600-50651200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr12:50642600-50652000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:50642800-50644200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:50642800-50649000	Weak transcription	Aorta	Aorta
40	chr12:50642800-50651200	Weak transcription	Brain Angular Gyrus	brain
41	chr12:50643000-50644000	Bivalent Enhancer	HUVEC	blood vessel
42	chr12:50643000-50645000	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr12:50643000-50645600	Weak transcription	HMEC	breast
44	chr12:50643000-50645600	Weak transcription	NHLF	lung
45	chr12:50643000-50646200	Enhancers	Duodenum Mucosa	Duodenum
46	chr12:50643000-50647400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr12:50643000-50648600	Weak transcription	Pancreas	Pancrea
48	chr12:50643000-50649400	Enhancers	Fetal Intestine Large	intestine
49	chr12:50643000-50651000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:50643000-50651200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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