Variant report

Variant	rs7423715
Chromosome Location	chr2:49071470-49071471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:49067039..49069722-chr2:49070584..49073190,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10495961	0.90[ASN][1000 genomes]
rs12991843	1.00[ASN][1000 genomes]
rs13009992	0.90[ASN][1000 genomes]
rs13014494	0.95[ASN][1000 genomes]
rs13015025	0.95[ASN][1000 genomes]
rs13025362	0.90[ASN][1000 genomes]
rs13026157	0.90[ASN][1000 genomes]
rs13030632	0.89[AFR][1000 genomes]
rs17483876	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17556035	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34339121	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34375934	0.90[ASN][1000 genomes]
rs34428472	1.00[ASN][1000 genomes]
rs4374422	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4432506	0.90[ASN][1000 genomes]
rs4449184	0.83[AFR][1000 genomes]
rs4491769	0.86[AFR][1000 genomes]
rs4525742	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4533511	0.90[ASN][1000 genomes]
rs4558635	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs55663001	0.90[ASN][1000 genomes]
rs55712456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55930451	0.90[ASN][1000 genomes]
rs55971673	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs56963017	0.90[ASN][1000 genomes]
rs57463767	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58176203	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58718281	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs59230684	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59263252	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60283047	0.88[AFR][1000 genomes]
rs60324887	0.85[ASN][1000 genomes]
rs60732263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61020573	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706022	0.90[ASN][1000 genomes]
rs67138907	0.90[ASN][1000 genomes]
rs6721247	0.90[ASN][1000 genomes]
rs6734547	0.90[ASN][1000 genomes]
rs72811814	0.87[AFR][1000 genomes]
rs72811828	0.87[AFR][1000 genomes]
rs72811832	0.85[ASN][1000 genomes]
rs72811860	0.90[ASN][1000 genomes]
rs72811867	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs72811870	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs72811872	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs72811873	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs72811885	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72811892	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72813716	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72823283	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567401	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591357	1.00[ASN][1000 genomes]
rs7594280	1.00[ASN][1000 genomes]
rs7594367	1.00[ASN][1000 genomes]
rs7597830	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv998864	chr2:49015878-49230000	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7423715	FOXN2	cis	parietal	SCAN
rs7423715	SRBD1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48994600-49080200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:49068800-49071600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:49070400-49071800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:49071200-49071600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:49071200-49072600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:49071200-49073200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:49071200-49073400	Enhancers	HMEC	breast
8	chr2:49071200-49073600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:49071400-49071800	Enhancers	HSMMtube	muscle
10	chr2:49071400-49072600	Enhancers	NH-A	brain
11	chr2:49071400-49072800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:49071400-49072800	Enhancers	HSMM	muscle
13	chr2:49071400-49073600	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links