Variant report

Variant	rs2517527
Chromosome Location	chr6:31021547-31021548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2394418	0.81[ASN][1000 genomes]
rs2394429	0.80[EUR][1000 genomes]
rs2508014	0.84[ASN][1000 genomes]
rs2517448	0.84[ASN][1000 genomes]
rs2517474	0.86[ASN][1000 genomes]
rs2517524	0.98[ASN][1000 genomes]
rs2517538	0.81[EUR][1000 genomes]
rs2517543	0.80[EUR][1000 genomes]
rs2517548	0.80[EUR][1000 genomes]
rs2517552	0.80[EUR][1000 genomes]
rs2523856	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2523857	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2523870	0.82[EUR][1000 genomes]
rs2523872	0.81[EUR][1000 genomes]
rs2523873	0.80[EUR][1000 genomes]
rs3132562	0.86[ASN][1000 genomes]
rs6457327	0.84[ASN][1000 genomes]
rs6905484	0.84[ASN][1000 genomes]
rs9263632	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv884130	chr6:31014305-31038756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv884131	chr6:31014305-31040725	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv884132	chr6:31014305-31057183	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv970677	chr6:31020994-31026537	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3370627	chr6:31021373-31025571	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2517527	HCG22	cis	Lymphoblastoid	GTEx
rs2517527	HIST1H1B	cis	cerebellum	SCAN
rs2517527	HCG22	cis	lymphoblastoid	seeQTL
rs2517527	TCF19	Cis_1M	lymphoblastoid	RTeQTL
rs2517527	hmm31752	cis	multi-tissue	Pritchard
rs2517527	HLA-C	cis	lymphoblastoid	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31009600-31027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:31010600-31021600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:31013800-31021600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:31016200-31021600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:31020800-31021600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:31020800-31022200	Enhancers	Fetal Heart	heart
7	chr6:31020800-31022400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:31020800-31022400	ZNF genes & repeats	GM12878-XiMat	blood
9	chr6:31021200-31021600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:31021200-31021600	Enhancers	Brain Germinal Matrix	brain
11	chr6:31021200-31022000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:31021200-31022200	Bivalent Enhancer	Fetal Stomach	stomach
13	chr6:31021400-31021600	Enhancers	Fetal Kidney	kidney
14	chr6:31021400-31022000	Enhancers	Fetal Brain Male	brain
15	chr6:31021400-31022200	Enhancers	Primary hematopoietic stem cells	blood
16	chr6:31021400-31022200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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