Variant report

Variant	rs2535329
Chromosome Location	chr6:30842674-30842675
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30709189..30710884-chr6:30841822..30843594,2	MCF-7	breast:
2	chr6:30831759..30834658-chr6:30842152..30844825,3	K562	blood:
3	chr6:30794216..30799803-chr6:30838849..30846731,16	K562	blood:
4	chr6:30707945..30712505-chr6:30840794..30847673,9	K562	blood:
5	chr6:30748393..30749996-chr6:30841265..30843895,2	K562	blood:
6	chr6:30840919..30843118-chr6:30894417..30896304,2	K562	blood:
7	chr6:30780598..30803497-chr6:30842531..30855110,80	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFTA2-10	chr6:30842554-30843695	ENSG00000237775.1

No data

Variant related genes	Relation type
ENSG00000214894	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000202241	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000228022	Chromatin interaction

Extended variants
information (count: 87 )
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];0.87[ASN][1000 genomes]
rs2074506	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2240804	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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];1.00[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]
rs2844655	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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:6 , 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	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
rs2535329	VARS2	cis	multi-tissue	Pritchard
rs2535329	VARSL	cis	uninvolved skin	skin_eQTL
rs2535329	GTF2H4///VARS2	Cis_1M	lymphoblastoid	RTeQTL
rs2535329	VARSL	cis	normal skin	skin_eQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30838800-30845000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr6:30838800-30845200	Weak transcription	Right Atrium	heart
3	chr6:30839800-30845000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr6:30840000-30845000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:30840800-30844800	Weak transcription	Thymus	Thymus
6	chr6:30841200-30843400	Weak transcription	Placenta	Placenta
7	chr6:30842400-30844600	Flanking Active TSS	K562	blood
8	chr6:30842400-30846000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:30842600-30845400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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