Variant report

Variant	rs12578863
Chromosome Location	chr12:122707270-122707271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:122707249-122707322	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:122707195-122707565	K562	blood:	n/a	n/a
3	POLR2A	chr12:122707152-122707618	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:122707165-122707590	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:122707190-122707563	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:122698849..122704062-chr12:122705218..122711671,13	MCF-7	breast:
2	chr12:122687145..122691347-chr12:122704062..122708275,6	MCF-7	breast:
3	chr12:122705056..122708320-chr12:122708578..122712255,7	MCF-7	breast:
4	chr12:122689976..122691920-chr12:122706553..122708365,2	MCF-7	breast:
5	chr12:122706789..122708655-chr12:122709178..122711069,2	K562	blood:
6	chr12:122236562..122239093-chr12:122704867..122707653,2	K562	blood:
7	chr12:122685663..122693033-chr12:122702446..122708793,8	K562	blood:

No data

Variant related genes	Relation type
DIABLO	TF binding region
ENSG00000139725	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000184047	Chromatin interaction
ENSG00000176383	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10848035	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11060167	0.88[EUR][1000 genomes]
rs11060333	0.87[EUR][1000 genomes]
rs12423987	0.82[EUR][1000 genomes]
rs12424872	0.92[ASN][1000 genomes]
rs12425684	0.84[EUR][1000 genomes]
rs12578739	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12578815	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12809220	0.87[EUR][1000 genomes]
rs12811503	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12814516	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12814554	0.82[EUR][1000 genomes]
rs12814923	0.85[EUR][1000 genomes]
rs12816400	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12816499	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12820704	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12822121	0.87[EUR][1000 genomes]
rs12824385	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12824925	0.84[EUR][1000 genomes]
rs12825008	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12825149	0.84[EUR][1000 genomes]
rs12825279	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12826834	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12827843	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12831210	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1512023	0.81[EUR][1000 genomes]
rs1967291	0.86[EUR][1000 genomes]
rs2068223	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271408	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271409	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2277333	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34383196	0.88[EUR][1000 genomes]
rs35030971	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35772530	0.89[EUR][1000 genomes]
rs35963777	0.84[EUR][1000 genomes]
rs3782153	0.80[EUR][1000 genomes]
rs3809116	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4758649	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4758677	0.88[EUR][1000 genomes]
rs6488906	0.86[EUR][1000 genomes]
rs6488909	0.85[EUR][1000 genomes]
rs7388	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12578863	MLXIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122689000-122709000	Weak transcription	Right Atrium	heart
2	chr12:122690600-122708000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:122690800-122708400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:122690800-122708800	Strong transcription	Fetal Brain Female	brain
5	chr12:122690800-122709400	Weak transcription	Stomach Mucosa	stomach
6	chr12:122691000-122707600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:122691000-122707800	Strong transcription	Thymus	Thymus
8	chr12:122691000-122708200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:122691000-122708800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:122691000-122708800	Strong transcription	A549	lung
11	chr12:122691200-122708000	Strong transcription	Brain Germinal Matrix	brain
12	chr12:122691200-122708000	Strong transcription	Stomach Smooth Muscle	stomach
13	chr12:122691200-122708400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr12:122691200-122708600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:122691200-122708800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:122691200-122709000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:122691200-122709200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr12:122691400-122707800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:122691400-122707800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:122691400-122708000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:122691400-122708200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr12:122691400-122708400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:122691400-122708400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:122691400-122708800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr12:122691400-122709000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:122691400-122709000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:122691400-122709000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:122691400-122709000	Strong transcription	Fetal Thymus	thymus
29	chr12:122691600-122707400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:122691600-122707400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr12:122691600-122707800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:122691600-122708000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:122691600-122708000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:122691600-122708400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:122691600-122708400	Strong transcription	Placenta	Placenta
36	chr12:122691600-122708400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:122691600-122709000	Strong transcription	Brain Hippocampus Middle	brain
38	chr12:122691600-122709000	Strong transcription	Fetal Muscle Leg	muscle
39	chr12:122691600-122709200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:122691800-122708000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:122691800-122708400	Strong transcription	Liver	Liver
42	chr12:122691800-122708600	Strong transcription	Rectal Smooth Muscle	rectum
43	chr12:122691800-122709000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr12:122691800-122709000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr12:122692000-122708400	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:122692200-122707600	Strong transcription	Osteobl	bone
47	chr12:122692200-122708400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:122692200-122709200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:122692400-122709200	Strong transcription	Fetal Lung	lung
50	chr12:122692600-122709000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links