Variant report

Variant	rs4744020
Chromosome Location	chr9:92776443-92776444
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr9:92774758..92776459-chr9:92788172..92789725,2	MCF-7	breast:
4	chr9:92775713..92778575-chr9:92781169..92782694,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130222	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10122211	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs10820817	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10820826	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10821471	0.86[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs10821474	0.86[CEU][hapmap]
rs10821478	0.83[AMR][1000 genomes]
rs10821479	0.83[AMR][1000 genomes]
rs10821505	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10821512	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10991697	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10991831	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs10993656	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1348383	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17361084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35216191	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4743823	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4743824	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4743827	0.94[JPT][hapmap]
rs4744040	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4744467	0.86[CEU][hapmap]
rs496129	0.84[AFR][1000 genomes]
rs552128	0.96[YRI][hapmap]
rs586750	0.90[AFR][1000 genomes]
rs6479330	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs652454	0.83[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs657899	0.81[MKK][hapmap]
rs661741	0.82[AFR][1000 genomes]
rs7021437	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7025825	0.85[CEU][hapmap]
rs7027342	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7030563	0.89[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs920753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs980139	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4744020	SYK	cis	cerebellum	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

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