Variant report

Variant	rs2245724
Chromosome Location	chr17:19493990-19493991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC47A1-1	chr17:19493768-19494003	NONHSAT146501

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1025904	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1034896	0.81[AMR][1000 genomes]
rs11650399	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11653348	0.81[AMR][1000 genomes]
rs12453452	0.90[CEU][hapmap]
rs12453474	0.90[CEU][hapmap]
rs12602112	0.94[CEU][hapmap];0.84[CHB][hapmap]
rs12937179	0.94[CEU][hapmap]
rs12949521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1800869	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs1806922	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072331	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2072333	0.80[EUR][1000 genomes]
rs2386144	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs2440161	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2891952	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34943952	0.81[AMR][1000 genomes]
rs35797108	0.81[AMR][1000 genomes]
rs4598966	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646797	0.81[EUR][1000 genomes]
rs4646798	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs66462929	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71369434	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7223468	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72840391	0.85[ASN][1000 genomes]
rs7503517	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs8064748	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9797254	0.81[AMR][1000 genomes]
rs9909440	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1056125	chr17:19484803-19536116	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1059195	chr17:19484803-19547972	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv2757654	chr17:19485735-19563766	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	esv2758679	chr17:19485735-19563766	Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv437815	chr17:19488851-19545834	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv437816	chr17:19488851-19545834	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1058163	chr17:19492744-19536116	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2245724	CTD-2104P17.1	cis	Nerve Tibial	GTEx
rs2245724	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19493200-19494800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr17:19493200-19499200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr17:19493400-19499200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:19493600-19494800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr17:19493800-19494600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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