Variant report

Variant	rs17040397
Chromosome Location	chr2:114553928-114553929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10167730	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10177576	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10179657	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10209330	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10496453	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123207	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11686297	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11694130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613159	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12711788	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2122097	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2442136	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2595140	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2595152	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687623	0.84[ASN][1000 genomes]
rs2687624	0.94[ASN][1000 genomes]
rs2687626	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2687627	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2687628	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2687630	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28451366	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34332133	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35734534	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4848349	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4848350	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849275	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4849277	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4849278	0.86[ASN][1000 genomes]
rs4849279	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6711542	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7600228	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17040397	RPL23AP7	cis	Artery Aorta	GTEx
rs17040397	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs17040397	RPL23AP7	cis	Muscle Skeletal	GTEx
rs17040397	RPL23AP7	cis	Whole Blood	GTEx
rs17040397	RPL23AP7	cis	lung	GTEx
rs17040397	RPL23AP7	cis	Artery Tibial	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114550000-114557000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:114550200-114555800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:114550200-114563800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:114552600-114554400	Enhancers	Fetal Intestine Small	intestine
5	chr2:114552800-114555000	Enhancers	Duodenum Mucosa	Duodenum
6	chr2:114553200-114554600	Weak transcription	Fetal Intestine Large	intestine
7	chr2:114553200-114557200	Weak transcription	Osteobl	bone
8	chr2:114553400-114554400	Weak transcription	Fetal Kidney	kidney
9	chr2:114553400-114554400	Weak transcription	HepG2	liver
10	chr2:114553400-114554600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:114553600-114557200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:114553800-114556600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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