Variant report

Variant	rs12043212
Chromosome Location	chr1:155964698-155964699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155902122..155904740-chr1:155963150..155964984,3	MCF-7	breast:
2	chr1:155902808..155904360-chr1:155964618..155967040,2	K562	blood:
3	chr1:155963540..155965817-chr1:155969797..155972514,2	MCF-7	breast:
4	chr1:155958825..155961254-chr1:155964574..155966369,2	MCF-7	breast:
5	chr1:155889869..155892126-chr1:155963034..155965549,2	K562	blood:

Variant related genes	Relation type
ENSG00000132680	Chromatin interaction
ENSG00000224276	Chromatin interaction
ENSG00000116584	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10908486	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11577179	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12032631	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12128541	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs1475766	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17381047	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17385065	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2297792	0.92[CEU][hapmap]
rs2364400	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2364401	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2886070	0.92[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34444588	0.80[AMR][1000 genomes]
rs34995046	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4330912	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4661079	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12043212	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12043212	GTF2IRD1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155954600-155970800	Weak transcription	NHEK	skin
2	chr1:155959200-155966000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:155959200-155978200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:155959400-155965000	Weak transcription	Pancreas	Pancrea
5	chr1:155959400-155965800	Weak transcription	HSMMtube	muscle
6	chr1:155959400-155970800	Weak transcription	Colonic Mucosa	Colon
7	chr1:155959400-155976600	Weak transcription	Aorta	Aorta
8	chr1:155959600-155965400	Weak transcription	Right Atrium	heart
9	chr1:155959600-155970400	Weak transcription	Stomach Mucosa	stomach
10	chr1:155959600-155971000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:155959600-155971800	Weak transcription	Gastric	stomach
12	chr1:155959800-155970400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:155959800-155970600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:155959800-155974600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:155960800-155965400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:155961000-155966000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:155961200-155965800	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:155961200-155965800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:155961200-155966000	Weak transcription	K562	blood
20	chr1:155961200-155974600	Weak transcription	Lung	lung
21	chr1:155961400-155965600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:155961400-155966000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:155961600-155969600	Weak transcription	Hela-S3	cervix
24	chr1:155962000-155965600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:155964400-155964800	Enhancers	Fetal Intestine Large	intestine
26	chr1:155964400-155964800	Enhancers	Fetal Intestine Small	intestine
27	chr1:155964400-155964800	Flanking Active TSS	HepG2	liver
28	chr1:155964400-155966400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:155964600-155964800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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