Variant report

No.	Distal block	Cell Line	Cell type
1	chr9:92213129..92215525-chr9:92775217..92778427,3	MCF-7	breast:
2	chr9:92219780..92221429-chr9:92776141..92778037,2	MCF-7	breast:
3	chr9:92775713..92778575-chr9:92781169..92782694,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130222	Chromatin interaction

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10117261	0.82[GIH][hapmap]
rs10820817	0.88[AFR][1000 genomes]
rs10820826	0.96[YRI][hapmap]
rs10821475	0.82[GIH][hapmap]
rs10821501	0.87[AFR][1000 genomes]
rs10991697	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1443364	0.87[AFR][1000 genomes]
rs17361084	0.84[AFR][1000 genomes]
rs4743823	0.92[YRI][hapmap]
rs4744020	0.83[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs496129	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs497510	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs552128	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs586750	0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs657899	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs661741	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs684476	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7021679	0.87[AFR][1000 genomes]
rs7030563	0.92[YRI][hapmap]
rs7866392	0.85[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap]
rs7874166	0.85[CEU][hapmap]
rs920753	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs652454	SYK	cis	cerebellum	SCAN
rs652454	ROR2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92771800-92781400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr9:92772200-92780800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:92773400-92780400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr9:92773800-92780800	Weak transcription	Primary B cells from cord blood	blood
5	chr9:92775400-92778000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:92775600-92778800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:92775600-92780400	Weak transcription	Lung	lung
8	chr9:92775800-92780600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:92775800-92780600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:92775800-92780800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr9:92775800-92780800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr9:92775800-92781200	Weak transcription	HSMMtube	muscle
13	chr9:92776000-92777800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:92776200-92776800	Enhancers	Esophagus	oesophagus
15	chr9:92776200-92778000	Enhancers	NHEK	skin
16	chr9:92776200-92778600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:92776400-92777800	Enhancers	HMEC	breast
18	chr9:92776400-92778800	Enhancers	Breast Myoepithelial Primary Cells	Breast

Quick Search: