Variant report

Variant	rs1041017
Chromosome Location	chr13:51482096-51482097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:51481879-51486954	GM12891	blood:	n/a	n/a
2	POLR2A	chr13:51481999-51482135	GM12878	blood:	n/a	n/a
3	CTCF	chr13:51482050-51482125	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51481866..51483659-chr13:51484720..51486682,2	K562	blood:
2	chr13:51473931..51480255-chr13:51481989..51485518,9	MCF-7	breast:

Variant related genes	Relation type
RNASEH2B	TF binding region
RNASEH2B-AS1	TF binding region
ENSG00000233672	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10400653	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs11616586	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11617366	0.83[ASW][hapmap];0.87[LWK][hapmap];0.83[AFR][1000 genomes]
rs11617765	0.90[EUR][1000 genomes]
rs11843914	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17074964	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67932352	0.81[AFR][1000 genomes]
rs73186372	0.80[AFR][1000 genomes]
rs7318931	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7323313	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7324091	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7335786	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7337118	0.88[EUR][1000 genomes]
rs74080784	1.00[EUR][1000 genomes]
rs7491820	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7992624	0.90[EUR][1000 genomes]
rs7993060	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8000150	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8001874	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8002319	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9526698	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9526703	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9526706	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9526709	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9526712	0.97[EUR][1000 genomes]
rs9535517	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs9535519	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9535522	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535529	0.89[LWK][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs9535537	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9591371	0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900077	chr13:51446114-51514831	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1041017	SETDB2	cis	parietal	SCAN
rs1041017	RNASEH2B	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51469000-51483400	Weak transcription	Fetal Lung	lung
2	chr13:51472800-51483400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:51475400-51483600	Weak transcription	Left Ventricle	heart
4	chr13:51476000-51483800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:51476400-51483400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr13:51477200-51483400	Weak transcription	Fetal Brain Female	brain
7	chr13:51480200-51483600	Weak transcription	Esophagus	oesophagus
8	chr13:51481600-51483200	Enhancers	Dnd41	blood
9	chr13:51481800-51482400	Enhancers	GM12878-XiMat	blood
10	chr13:51481800-51483200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr13:51482000-51482200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr13:51482000-51483000	Enhancers	Primary B cells from cord blood	blood
13	chr13:51482000-51483200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr13:51482000-51483200	Enhancers	Fetal Thymus	thymus
15	chr13:51482000-51483400	Weak transcription	Primary T cells from cord blood	blood
16	chr13:51482000-51483400	Enhancers	Primary hematopoietic stem cells	blood
17	chr13:51482000-51483400	Weak transcription	Fetal Intestine Large	intestine
18	chr13:51482000-51483400	Enhancers	Thymus	Thymus

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