Variant report

Variant	rs3132581
Chromosome Location	chr6:30913458-30913459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30874607..30877017-chr6:30913155..30915991,2	K562	blood:
2	chr6:30912250..30916872-chr6:30917864..30923699,9	K562	blood:
3	chr6:30876567..30879168-chr6:30912847..30914474,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFTA2-3	chr6:30913264-30914370	l_3162_chr6:30913263-30924009_76bGuttman_hES

Variant related genes	Relation type
ENSG00000233529	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000264731	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10456390	0.86[ASN][1000 genomes]
rs1049633	0.81[AMR][1000 genomes]
rs11757361	1.00[ASN][1000 genomes]
rs12193866	0.86[ASN][1000 genomes]
rs12196019	0.86[ASN][1000 genomes]
rs12196237	0.80[ASN][1000 genomes]
rs12197587	0.86[ASN][1000 genomes]
rs12201301	0.86[ASN][1000 genomes]
rs12202207	0.86[ASN][1000 genomes]
rs12207025	0.86[ASN][1000 genomes]
rs12212799	0.80[ASN][1000 genomes]
rs1264308	0.81[AMR][1000 genomes]
rs1264325	0.81[AMR][1000 genomes]
rs1264347	0.81[AMR][1000 genomes]
rs1264350	0.88[EUR][1000 genomes]
rs13191523	0.86[ASN][1000 genomes]
rs13212987	0.86[ASN][1000 genomes]
rs1634716	0.81[AMR][1000 genomes]
rs1634721	0.81[AMR][1000 genomes]
rs17189812	0.80[ASN][1000 genomes]
rs17189826	0.86[ASN][1000 genomes]
rs2263298	0.81[AMR][1000 genomes]
rs2517578	0.81[AMR][1000 genomes]
rs2535328	0.81[AMR][1000 genomes]
rs2535332	0.81[AMR][1000 genomes]
rs2535334	0.81[AMR][1000 genomes]
rs2535340	0.81[AMR][1000 genomes]
rs2844656	0.81[AMR][1000 genomes]
rs3094086	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094088	0.81[AMR][1000 genomes]
rs3095152	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3095153	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3095156	0.81[AMR][1000 genomes]
rs3130574	0.81[AMR][1000 genomes]
rs3130781	0.82[ASN][1000 genomes]
rs3131781	0.81[AMR][1000 genomes]
rs3131920	0.81[AMR][1000 genomes]
rs3131921	0.86[EUR][1000 genomes]
rs3132577	0.81[AMR][1000 genomes]
rs3132580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73727119	1.00[ASN][1000 genomes]
rs73727120	1.00[ASN][1000 genomes]
rs73727123	1.00[ASN][1000 genomes]
rs73727137	1.00[ASN][1000 genomes]
rs886422	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined)	23453885	GWAS catalog

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3132581	BTN3A2	cis	multi-tissue	Pritchard
rs3132581	HLA-DQB1	cis	multi-tissue	Pritchard
rs3132581	VARSL	cis	multi-tissue	Pritchard
rs3132581	HLA-A	cis	brain	seeQTL
rs3132581	C6orf1	cis	parietal	SCAN
rs3132581	HIST1H2BM	cis	cerebellum	SCAN
rs3132581	HLA-H	cis	multi-tissue	Pritchard
rs3132581	HLA-C	cis	multi-tissue	Pritchard
rs3132581	HLA-A	cis	multi-tissue	Pritchard
rs3132581	HIST1H2AM	cis	cerebellum	SCAN
rs3132581	HCG27	cis	multi-tissue	Pritchard
rs3132581	HLA-DRB1	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30910400-30913800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:30911000-30913800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr6:30911000-30913800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:30911000-30919000	Weak transcription	Right Atrium	heart
5	chr6:30911200-30913800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:30911200-30914000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:30911200-30914000	Weak transcription	Stomach Mucosa	stomach
8	chr6:30911400-30915000	Weak transcription	Gastric	stomach

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