Variant report

Variant	rs10942252
Chromosome Location	chr5:27477815-27477816
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf17-8	chr5:27477746-27477908	ENSG00000250337
2	lnc-C5orf17-8	chr5:27476833-27477908	XLOC_004323

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10041105	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10043278	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045438	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059093	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10472571	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10472572	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10473841	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10473842	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942259	0.89[EUR][1000 genomes]
rs11741407	0.89[EUR][1000 genomes]
rs11742648	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11948589	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11951177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12518672	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12653531	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655436	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12656885	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12659482	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12659906	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13169053	0.86[EUR][1000 genomes]
rs2329584	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329622	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2329626	0.89[EUR][1000 genomes]
rs35172002	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56110024	0.89[EUR][1000 genomes]
rs62352269	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62354163	0.94[EUR][1000 genomes]
rs6452387	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6452390	0.89[EUR][1000 genomes]
rs6881731	0.89[EUR][1000 genomes]
rs6895283	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881286	chr5:27135351-27770554	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv880298	chr5:27193573-27659111	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv880326	chr5:27193573-27743375	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv880623	chr5:27279981-27559659	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv881318	chr5:27323746-27559659	Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv881503	chr5:27344037-27510050	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv881475	chr5:27376682-27510050	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv881003	chr5:27376682-27539490	Enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv880935	chr5:27376682-27559659	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv880535	chr5:27376682-27706007	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv881089	chr5:27387385-27478198	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv881139	chr5:27388559-27539490	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv880496	chr5:27388559-27559659	Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv880940	chr5:27388559-27611431	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv880999	chr5:27388559-27770554	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv880926	chr5:27401935-27539490	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv881221	chr5:27401935-27660532	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv881125	chr5:27406164-27622177	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	nsv880660	chr5:27418887-27510050	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv880726	chr5:27424981-27539490	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv880474	chr5:27424981-27559659	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	nsv880869	chr5:27424981-27684515	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv597681	chr5:27426728-27526060	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
24	nsv1030914	chr5:27458599-27502029	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
25	nsv881364	chr5:27464184-27611431	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:27474400-27478000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
2	chr5:27474400-27478600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
3	chr5:27474600-27478000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
4	chr5:27474600-27478800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:27474800-27478000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
6	chr5:27474800-27478200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
7	chr5:27475000-27478200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:27475200-27478200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
9	chr5:27475600-27478000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:27475600-27478000	ZNF genes & repeats	GM12878-XiMat	blood
11	chr5:27475600-27486800	Strong transcription	A549	lung
12	chr5:27475800-27478000	Genic enhancers	HepG2	liver
13	chr5:27476400-27478000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:27477000-27478000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:27477000-27478000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:27477000-27478600	Strong transcription	Hela-S3	cervix
17	chr5:27477000-27478800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:27477200-27478000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:27477400-27478800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:27477400-27480000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:27477600-27480000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:27477800-27478000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:27477800-27478800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:27477800-27481200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links