Variant report

Variant	rs12121071
Chromosome Location	chr1:226290675-226290676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226248690..226250361-chr1:226290467..226292508,2	MCF-7	breast:
2	chr1:226286017..226288107-chr1:226288751..226292148,3	K562	blood:
3	chr1:226286017..226288107-chr1:226288751..226291625,2	K562	blood:

Variant related genes	Relation type
ENSG00000272562	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10915933	0.82[ASN][1000 genomes]
rs10915934	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10915936	0.88[EUR][1000 genomes]
rs10915938	0.82[ASN][1000 genomes]
rs10915939	0.82[ASN][1000 genomes]
rs10915940	0.80[ASN][1000 genomes]
rs11577282	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12026319	0.92[ASN][1000 genomes]
rs12117683	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12117819	0.89[EUR][1000 genomes]
rs12130296	0.82[ASN][1000 genomes]
rs12131977	0.89[ASN][1000 genomes]
rs12144544	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1355391	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6693755	0.85[EUR][1000 genomes]
rs7515023	0.88[EUR][1000 genomes]
rs7552463	0.87[EUR][1000 genomes]
rs9645314	0.81[ASN][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	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	esv1792510	chr1:226277560-226323824	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12121071	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs12121071	H3F3A	cis	Esophagus Mucosa	GTEx
rs12121071	H3F3A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226281200-226295000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:226286200-226297200	Weak transcription	Hela-S3	cervix
3	chr1:226286600-226291800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:226288400-226291800	Weak transcription	HMEC	breast
5	chr1:226288600-226292000	Weak transcription	HSMMtube	muscle
6	chr1:226288600-226292400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:226288600-226296600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:226288800-226292200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:226288800-226292400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:226288800-226292400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:226288800-226292600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:226289000-226291800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:226289000-226292000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:226289000-226292000	Weak transcription	Placenta	Placenta
15	chr1:226289000-226292000	Weak transcription	K562	blood
16	chr1:226289000-226292200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:226289000-226292200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:226289000-226292200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:226289000-226292200	Weak transcription	Lung	lung
20	chr1:226289000-226292400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:226289000-226292400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:226289000-226292400	Weak transcription	HSMM	muscle
23	chr1:226289000-226292400	Weak transcription	Osteobl	bone
24	chr1:226289000-226295200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:226289000-226295200	Weak transcription	Stomach Mucosa	stomach
26	chr1:226289000-226295800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:226289000-226296400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:226289000-226296400	Weak transcription	Right Atrium	heart
29	chr1:226289000-226296600	Weak transcription	Right Ventricle	heart
30	chr1:226289000-226296600	Weak transcription	NHLF	lung
31	chr1:226289000-226297000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:226289000-226297000	Weak transcription	HUVEC	blood vessel
33	chr1:226289200-226292400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:226289200-226292400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:226289200-226295200	Weak transcription	Esophagus	oesophagus
36	chr1:226289200-226297000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links