Variant report

Variant	rs2535340
Chromosome Location	chr6:30838497-30838498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1049633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059612	0.90[AMR][1000 genomes]
rs1264308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1264347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1264351	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1264361	0.87[EUR][1000 genomes]
rs1264373	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1634716	1.00[AMR][1000 genomes]
rs1634721	1.00[AMR][1000 genomes]
rs1634726	0.89[AMR][1000 genomes]
rs2263298	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2517546	0.90[AMR][1000 genomes]
rs2517578	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2524266	0.92[EUR][1000 genomes]
rs2535328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535332	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535334	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2844656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844661	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3094088	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095152	0.81[AMR][1000 genomes]
rs3095153	0.81[AMR][1000 genomes]
rs3095156	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3095326	0.81[AMR][1000 genomes]
rs3095328	0.81[AMR][1000 genomes]
rs3095332	0.81[AMR][1000 genomes]
rs3129973	0.81[AMR][1000 genomes]
rs3129974	0.81[AMR][1000 genomes]
rs3129980	0.80[EUR][1000 genomes]
rs3129982	0.80[EUR][1000 genomes]
rs3129983	0.80[EUR][1000 genomes]
rs3129984	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3129985	0.80[EUR][1000 genomes]
rs3130641	0.83[EUR][1000 genomes]
rs3130668	0.81[AMR][1000 genomes]
rs3131041	0.82[EUR][1000 genomes]
rs3131044	0.80[EUR][1000 genomes]
rs3131045	0.80[EUR][1000 genomes]
rs3131047	0.80[EUR][1000 genomes]
rs3131049	0.80[EUR][1000 genomes]
rs3131050	0.80[EUR][1000 genomes]
rs3131052	0.81[EUR][1000 genomes]
rs3131055	0.80[EUR][1000 genomes]
rs3131058	0.80[EUR][1000 genomes]
rs3131060	0.80[EUR][1000 genomes]
rs3131781	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3132577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132580	0.81[AMR][1000 genomes]
rs3132581	0.81[AMR][1000 genomes]
rs3132600	0.81[EUR][1000 genomes]
rs886422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886424	0.87[EUR][1000 genomes]
rs886425	0.87[EUR][1000 genomes]
rs9262200	0.80[EUR][1000 genomes]
rs9262202	0.80[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2535340	C6orf1	cis	parietal	SCAN
rs2535340	HIST1H2BM	cis	cerebellum	SCAN
rs2535340	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30837800-30838800	ZNF genes & repeats	Placenta	Placenta
2	chr6:30838200-30839000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:30838400-30838800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr6:30838400-30838800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr6:30838400-30839000	ZNF genes & repeats	Thymus	Thymus
6	chr6:30838400-30840800	ZNF genes & repeats	Dnd41	blood

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