Variant report

Variant	rs3213541
Chromosome Location	chr6:100896243-100896244
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:100895834..100897830-chr6:100900574..100903178,3	K562	blood:
2	chr6:100895834..100897830-chr6:100900625..100903178,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1506080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17060614	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17060615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847912	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1857859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs241812	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs3734353	0.84[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798488	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798492	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3798495	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798497	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3830139	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs767933	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7741057	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757905	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390379	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv515895	chr6:100868779-100910798	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
6	nsv533053	chr6:100883636-100911512	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3213541	SNORA26	trans	lymphoblastoid	seeQTL
rs3213541	PRDM13	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100894000-100897600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:100894400-100896400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr6:100894400-100896400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:100894400-100896800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:100894400-100897600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:100894400-100898000	Strong transcription	Muscle Satellite Cultured Cells	--
7	chr6:100894600-100901600	Weak transcription	Psoas Muscle	Psoas
8	chr6:100895000-100896400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
9	chr6:100895000-100896400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:100895000-100896400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:100895000-100896400	ZNF genes & repeats	Spleen	Spleen
12	chr6:100895200-100897400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:100895200-100897400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:100895200-100897600	Bivalent Enhancer	Right Ventricle	heart
15	chr6:100895400-100896400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:100895400-100897200	Strong transcription	HSMM	muscle
17	chr6:100895400-100897400	Strong transcription	HSMMtube	muscle
18	chr6:100895400-100898400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:100895400-100898400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:100895600-100896400	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:100895600-100896400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:100895600-100897200	Weak transcription	Right Atrium	heart
23	chr6:100895800-100896400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
24	chr6:100895800-100897600	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:100896000-100896400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:100896000-100896400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:100896000-100896400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
28	chr6:100896200-100896800	Strong transcription	Pancreas	Pancrea
29	chr6:100896200-100897400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:100896200-100897400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:100896200-100897800	Strong transcription	Pancreatic Islets	Pancreatic Islet

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