Variant report

Variant	rs2844655
Chromosome Location	chr6:30837538-30837539
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30837036..30839177-chr6:30843393..30845146,2	K562	blood:
2	chr6:30830259..30832275-chr6:30835833..30838069,3	K562	blood:
3	chr6:30521625..30525258-chr6:30837019..30840753,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFTA2-10	chr6:30834759-30837610	ENSG00000237775.1

Variant related genes	Relation type
ENSG00000202241	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000204576	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1264297	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264298	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264299	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264300	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264301	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264302	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264303	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264305	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264307	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264309	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264317	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264320	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264332	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1264342	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17189763	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074506	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2240804	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249459	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2252760	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2252856	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2252863	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2394856	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2517449	0.95[EUR][1000 genomes]
rs2517457	0.92[EUR][1000 genomes]
rs2517461	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2517462	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2517463	0.93[EUR][1000 genomes]
rs2517466	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2517468	0.97[EUR][1000 genomes]
rs2517573	0.87[EUR][1000 genomes]
rs2517575	0.88[EUR][1000 genomes]
rs2517577	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2517579	0.81[AMR][1000 genomes]
rs2517580	0.82[AMR][1000 genomes]
rs2517582	0.83[EUR][1000 genomes]
rs2532920	0.91[EUR][1000 genomes]
rs2532921	0.94[EUR][1000 genomes]
rs2532927	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2532928	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2532929	0.87[EUR][1000 genomes]
rs2532930	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2532933	0.94[EUR][1000 genomes]
rs2532935	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2532936	0.97[EUR][1000 genomes]
rs2532937	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2532938	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2532939	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2532940	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2532942	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2532943	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535325	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535326	0.89[EUR][1000 genomes]
rs2535327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535330	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535331	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2535335	0.89[EUR][1000 genomes]
rs2535336	0.89[EUR][1000 genomes]
rs2535337	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2535339	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2844652	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2844654	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2844658	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2844662	0.88[EUR][1000 genomes]
rs2844663	0.87[EUR][1000 genomes]
rs2844664	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2844698	0.82[EUR][1000 genomes]
rs2844699	0.87[EUR][1000 genomes]
rs2844702	0.96[EUR][1000 genomes]
rs3130657	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs753726	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7738138	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7756286	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs887381	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262288	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262289	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262290	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262291	0.91[EUR][1000 genomes]
rs9262292	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262293	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262294	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv884108	chr6:30821187-30838497	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv884109	chr6:30824532-30872203	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2844655	VARS2	cis	multi-tissue	Pritchard
rs2844655	VARSL	cis	uninvolved skin	skin_eQTL
rs2844655	VARSL	cis	normal skin	skin_eQTL
rs2844655	GTF2H4///VARS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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