Variant report

Variant	rs12024849
Chromosome Location	chr1:169464278-169464279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169463126..169465352-chr1:169467023..169469114,3	K562	blood:
2	chr1:169463675..169465938-chr1:169469151..169470864,2	K562	blood:
3	chr1:169462387..169464919-chr1:169482151..169485125,2	MCF-7	breast:
4	chr1:169463786..169466732-chr1:169496061..169498768,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10800452	0.85[ASN][1000 genomes]
rs10919177	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10919184	0.85[ASN][1000 genomes]
rs10919185	0.85[ASN][1000 genomes]
rs12022575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12025910	0.95[ASN][1000 genomes]
rs12239964	0.90[ASN][1000 genomes]
rs12405595	0.95[ASN][1000 genomes]
rs12563507	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1557571	0.85[ASN][1000 genomes]
rs1800595	0.85[ASN][1000 genomes]
rs1894691	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1894703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2227243	0.95[ASN][1000 genomes]
rs2285212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2301516	0.85[ASN][1000 genomes]
rs2301519	0.85[ASN][1000 genomes]
rs2301520	0.85[ASN][1000 genomes]
rs2420134	0.95[ASN][1000 genomes]
rs2420135	0.95[ASN][1000 genomes]
rs35337011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3766104	0.95[ASN][1000 genomes]
rs4440913	0.95[ASN][1000 genomes]
rs6013	0.95[ASN][1000 genomes]
rs6018	0.85[ASN][1000 genomes]
rs6024	0.85[ASN][1000 genomes]
rs6027	0.95[ASN][1000 genomes]
rs72706088	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72708008	0.95[ASN][1000 genomes]
rs72708013	0.95[ASN][1000 genomes]
rs72708039	0.85[ASN][1000 genomes]
rs916439	0.85[ASN][1000 genomes]
rs9332601	0.85[ASN][1000 genomes]
rs9332609	0.85[ASN][1000 genomes]
rs9332614	0.80[ASN][1000 genomes]
rs9332629	0.85[ASN][1000 genomes]
rs9332639	0.90[ASN][1000 genomes]
rs9332641	0.90[ASN][1000 genomes]
rs9332646	0.90[ASN][1000 genomes]
rs9332654	0.90[ASN][1000 genomes]
rs9332659	0.90[ASN][1000 genomes]
rs9332661	0.95[ASN][1000 genomes]
rs9332673	0.95[ASN][1000 genomes]
rs9332676	0.95[ASN][1000 genomes]
rs966751	0.95[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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12024849	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169457000-169464400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr1:169457800-169464400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:169458600-169464800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:169461600-169464400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:169462200-169465400	Enhancers	Placenta	Placenta
6	chr1:169463800-169464600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr1:169464000-169464400	Weak transcription	Fetal Heart	heart
8	chr1:169464000-169467200	Weak transcription	HepG2	liver
9	chr1:169464200-169465000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:169464200-169465400	Enhancers	HMEC	breast
11	chr1:169464200-169465600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:169464200-169465600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:169464200-169465800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:169464200-169465800	Enhancers	NHEK	skin

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