Variant report

Variant	rs2240804
Chromosome Location	chr6:30920890-30920891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30887250..30888956-chr6:30920094..30923079,2	MCF-7	breast:
2	chr6:30919991..30921780-chr6:30922637..30925077,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFTA2-3	chr6:30920844-30920981	ENSG00000233529.1

Variant related genes	Relation type
ENSG00000137411	Chromatin interaction
ENSG00000233529	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1264297	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264298	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264299	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264300	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1264301	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264302	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264303	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264305	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264307	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264309	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264317	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264320	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1264332	0.96[EUR][1000 genomes]
rs1264342	0.90[EUR][1000 genomes]
rs17189763	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2074506	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2249459	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2252760	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2252856	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2252863	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2394856	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2517449	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2517457	0.92[EUR][1000 genomes]
rs2517461	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2517462	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2517463	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2517466	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2517468	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2517573	0.87[EUR][1000 genomes]
rs2517575	0.87[EUR][1000 genomes]
rs2517577	0.96[EUR][1000 genomes]
rs2517582	0.82[EUR][1000 genomes]
rs2532920	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2532921	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2532927	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2532928	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2532929	0.87[EUR][1000 genomes]
rs2532930	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2532933	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2532935	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2532936	0.96[EUR][1000 genomes]
rs2532937	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2532938	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2532939	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2532940	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2532942	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2532943	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2535325	0.96[EUR][1000 genomes]
rs2535326	0.89[EUR][1000 genomes]
rs2535327	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535329	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535330	0.96[EUR][1000 genomes]
rs2535331	0.94[EUR][1000 genomes]
rs2535335	0.89[EUR][1000 genomes]
rs2535336	0.89[EUR][1000 genomes]
rs2535337	0.96[EUR][1000 genomes]
rs2535339	0.96[EUR][1000 genomes]
rs2844652	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2844654	0.96[EUR][1000 genomes]
rs2844655	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2844658	0.96[EUR][1000 genomes]
rs2844662	0.87[EUR][1000 genomes]
rs2844663	0.87[EUR][1000 genomes]
rs2844664	0.94[EUR][1000 genomes]
rs2844698	0.83[EUR][1000 genomes]
rs2844699	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2844702	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3130657	0.96[EUR][1000 genomes]
rs753726	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7738138	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7756286	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs887381	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9262288	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9262289	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9262290	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9262291	0.90[EUR][1000 genomes]
rs9262292	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9262293	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9262294	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv462743	chr6:30905313-30957766	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv601483	chr6:30905313-30957766	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv823473	chr6:30920117-30921002	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv462744	chr6:30920890-30955681	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv601484	chr6:30920890-30955681	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2240804	VARSL	cis	normal skin	skin_eQTL
rs2240804	GTF2H4///VARS2	Cis_1M	lymphoblastoid	RTeQTL
rs2240804	HCG22	cis	lymphoblastoid	seeQTL
rs2240804	GRM4	cis	parietal	SCAN
rs2240804	VARSL	cis	uninvolved skin	skin_eQTL
rs2240804	HIST1H2BL	cis	parietal	SCAN
rs2240804	DDAH2	cis	lymphoblastoid	seeQTL
rs2240804	VARS2	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30913600-30922800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr6:30915400-30923000	Weak transcription	Gastric	stomach
3	chr6:30919400-30923000	Weak transcription	Right Atrium	heart
4	chr6:30919600-30921000	Enhancers	GM12878-XiMat	blood
5	chr6:30920200-30922800	Weak transcription	Brain Substantia Nigra	brain
6	chr6:30920200-30922800	Weak transcription	Stomach Mucosa	stomach
7	chr6:30920600-30921000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr6:30920800-30921000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:30920800-30921000	Enhancers	Ovary	ovary
10	chr6:30920800-30921000	Enhancers	Spleen	Spleen

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