Variant report

Variant	rs3132580
Chromosome Location	chr6:30920124-30920125
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:

Variant related genes	Relation type
ENSG00000233529	Chromatin interaction
ENSG00000137411	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

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]
rs3132581	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:10 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Idiopathic membranous nephropathy	21323541	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3132580	HIST1H2BM	cis	cerebellum	SCAN
rs3132580	HIST1H2AM	cis	cerebellum	SCAN
rs3132580	C6orf1	cis	parietal	SCAN
rs3132580	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 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	chr6:30918800-30920200	Strong transcription	Stomach Mucosa	stomach
4	chr6:30919400-30923000	Weak transcription	Right Atrium	heart
5	chr6:30919600-30921000	Enhancers	GM12878-XiMat	blood
6	chr6:30919800-30920200	Active TSS	Brain Substantia Nigra	brain

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