Variant report

Variant	rs12144544
Chromosome Location	chr1:226284680-226284681
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226248606..226253173-chr1:226284657..226288071,4	MCF-7	breast:
2	chr1:226283199..226285727-chr1:226307856..226310769,2	K562	blood:
3	chr1:226283361..226286277-chr1:226307915..226310470,2	MCF-7	breast:
4	chr1:226260420..226263013-chr1:226284243..226287339,3	K562	blood:
5	chr1:226263073..226265688-chr1:226283492..226286282,2	K562	blood:
6	chr1:226260970..226263013-chr1:226283017..226285743,2	K562	blood:
7	chr1:226271135..226274026-chr1:226283314..226286271,2	K562	blood:
8	chr1:226283335..226286011-chr1:226296235..226298970,2	K562	blood:

No data

No data

No data

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10915933	0.86[ASN][1000 genomes]
rs10915934	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11577282	0.87[EUR][1000 genomes]
rs12026319	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12117683	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12117819	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12121071	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12131977	0.81[ASN][1000 genomes]
rs1355391	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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
rs12144544	H3F3A	cis	Skin Sun Exposed Lower leg	GTEx
rs12144544	H3F3A	cis	Esophagus Mucosa	GTEx
rs12144544	H3F3A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226271800-226286200	Weak transcription	Ovary	ovary
2	chr1:226271800-226288000	Weak transcription	Right Atrium	heart
3	chr1:226271800-226288400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:226272000-226285400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:226272000-226287800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:226272000-226288200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:226278800-226287600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:226281200-226295000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:226281400-226285400	Weak transcription	K562	blood
10	chr1:226283800-226285800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:226284000-226284800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:226284000-226285400	Enhancers	HMEC	breast
13	chr1:226284000-226285400	Enhancers	NHEK	skin
14	chr1:226284000-226285800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:226284000-226286200	Enhancers	Esophagus	oesophagus
16	chr1:226284400-226286000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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