Variant report

Variant	rs12026057
Chromosome Location	chr1:155889327-155889328
allele	C/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	chr1:155888434-155889367	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:155888772-155889529	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:155887544-155889563	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:155888784-155889388	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:155888951-155889362	K562	blood:	n/a	n/a
6	POLR2A	chr1:155888898-155889363	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155889116..155891316-chr1:155948021..155950216,2	K562	blood:

Variant related genes	Relation type
KIAA0907	TF binding region
ENSG00000116584	Chromatin interaction
ENSG00000273002	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10796955	0.84[AMR][1000 genomes]
rs10908483	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12037177	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12144175	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12568523	0.86[EUR][1000 genomes]
rs1889532	0.84[AMR][1000 genomes]
rs1889533	0.84[AMR][1000 genomes]
rs2016251	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2282301	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2297649	0.84[AMR][1000 genomes]
rs66466805	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66669006	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6667652	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6670477	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6696019	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72708205	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7528441	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7545308	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs867548	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs867549	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs867550	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs915181	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12026057	GON4L	Cis_1M	lymphoblastoid	RTeQTL
rs12026057	RIT1	cis	Thyroid	GTEx
rs12026057	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155881400-155889600	Weak transcription	Pancreas	Pancrea
2	chr1:155881400-155890400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:155881600-155889800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:155881600-155890800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:155881800-155893600	Strong transcription	HMEC	breast
6	chr1:155881800-155898800	Strong transcription	HUVEC	blood vessel
7	chr1:155881800-155899800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:155881800-155900600	Strong transcription	Fetal Muscle Leg	muscle
9	chr1:155881800-155901200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:155881800-155901200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:155882000-155898800	Strong transcription	NH-A	brain
12	chr1:155882000-155899400	Strong transcription	Fetal Intestine Large	intestine
13	chr1:155882000-155899800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:155882000-155900000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:155882000-155900000	Strong transcription	Liver	Liver
16	chr1:155882000-155900200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:155882000-155900400	Strong transcription	Primary B cells from cord blood	blood
18	chr1:155882000-155900600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:155882000-155900600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:155882000-155900600	Strong transcription	Placenta	Placenta
21	chr1:155882000-155900600	Strong transcription	Fetal Stomach	stomach
22	chr1:155882000-155900600	Strong transcription	Left Ventricle	heart
23	chr1:155882000-155900800	Strong transcription	Thymus	Thymus
24	chr1:155882000-155901000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:155882000-155901400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:155882000-155901400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr1:155882200-155898600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:155882200-155900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:155882200-155900600	Strong transcription	Fetal Thymus	thymus
30	chr1:155882200-155901000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:155882200-155901000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:155882200-155901200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:155882200-155901400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:155882200-155901400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:155882200-155901400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:155882200-155903000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:155882400-155893800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:155882400-155898800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:155882400-155900000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:155882400-155900000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:155882400-155900000	Strong transcription	Adipose Nuclei	Adipose
42	chr1:155882400-155900200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr1:155882600-155889400	Strong transcription	Colon Smooth Muscle	Colon
44	chr1:155882600-155898800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:155882600-155899000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:155882600-155899000	Strong transcription	NHEK	skin
47	chr1:155882600-155900200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:155882600-155900200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:155882600-155901600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:155882600-155901600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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