Variant report

Variant	rs1319677
Chromosome Location	chr9:93565999-93566000
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:93564315..93567256-chr9:93578660..93580228,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10448310	0.81[ASN][1000 genomes]
rs10993693	0.91[CHB][hapmap];0.85[CHD][hapmap]
rs12350798	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs1333630	0.91[CHB][hapmap]
rs1333632	0.86[ASN][1000 genomes]
rs1333634	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1333635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1333637	0.81[ASN][1000 genomes]
rs188313	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2562396	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562397	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2613308	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2774260	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2780701	0.95[CHB][hapmap];0.92[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2780702	0.82[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290266	0.86[AMR][1000 genomes]
rs290268	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs290271	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs290274	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs290276	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs290987	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290988	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290989	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290990	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290991	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs290993	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290994	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs290997	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291006	0.86[AMR][1000 genomes]
rs772407	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7856021	0.91[CHB][hapmap]
rs914925	0.91[CHB][hapmap]
rs94626	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893567	chr9:93519280-93609668	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv893569	chr9:93552550-93587089	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv1813758	chr9:93557698-93573095	Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv275555	chr9:93565999-93570451	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1319677	SYK	cis	lymphoblastoid	seeQTL
rs1319677	SYK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93563200-93568000	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr9:93563800-93566600	Active TSS	K562	blood
3	chr9:93563800-93566800	Active TSS	Duodenum Mucosa	Duodenum
4	chr9:93563800-93567000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:93563800-93567200	Active TSS	GM12878-XiMat	blood
6	chr9:93563800-93567400	Active TSS	Thymus	Thymus
7	chr9:93563800-93567600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr9:93564000-93566000	Active TSS	Primary monocytes fromperipheralblood	blood
9	chr9:93564600-93566400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:93564600-93567000	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr9:93564600-93567400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:93564600-93567400	Active TSS	Fetal Thymus	thymus
13	chr9:93564600-93567400	Weak transcription	Gastric	stomach
14	chr9:93564600-93567400	Weak transcription	Pancreas	Pancrea
15	chr9:93564600-93567400	Weak transcription	Spleen	Spleen
16	chr9:93564600-93567600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:93564600-93568600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:93564600-93572000	Weak transcription	Lung	lung
19	chr9:93564800-93566600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:93564800-93566800	Weak transcription	Right Atrium	heart
21	chr9:93564800-93567800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:93565000-93566600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:93565000-93567400	Weak transcription	Stomach Mucosa	stomach
24	chr9:93565000-93569400	Weak transcription	Primary T cells from cord blood	blood
25	chr9:93565000-93609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:93565200-93566400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:93565200-93566400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr9:93565200-93567800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr9:93565200-93568400	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr9:93565400-93566000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr9:93565400-93566200	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr9:93565400-93566200	Enhancers	Fetal Kidney	kidney
33	chr9:93565400-93566400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:93565400-93566600	Weak transcription	Fetal Intestine Small	intestine
35	chr9:93565400-93567400	Weak transcription	Fetal Stomach	stomach
36	chr9:93565400-93567600	Enhancers	NHEK	skin
37	chr9:93565400-93570600	Weak transcription	HMEC	breast
38	chr9:93565400-93570800	Weak transcription	Placenta	Placenta
39	chr9:93565400-93577000	Weak transcription	Colonic Mucosa	Colon
40	chr9:93565600-93566000	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr9:93565600-93567000	Weak transcription	Fetal Intestine Large	intestine
42	chr9:93565600-93567800	Enhancers	Rectal Mucosa Donor 31	rectum

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