Variant report

Variant	rs12553524
Chromosome Location	chr9:93569646-93569647
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:93569248..93572925-chr9:93585588..93587867,3	K562	blood:
2	chr9:93562623..93567761-chr9:93568030..93571323,5	K562	blood:
3	chr9:93561656..93565893-chr9:93566155..93575937,12	MCF-7	breast:
4	chr9:93569272..93571391-chr9:93577022..93579806,2	K562	blood:

Variant related genes	Relation type
ENSG00000165025	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10821508	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10993697	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.88[ASN][1000 genomes]
rs10993698	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs11788207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12551275	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1460834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1460835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16906825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16906859	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs17488335	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2042983	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042984	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162977	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780702	0.90[YRI][hapmap]
rs290233	0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs290239	0.90[ASN][1000 genomes]
rs290240	0.92[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs290241	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3789890	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789892	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789893	0.89[ASN][1000 genomes]
rs4002564	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4002565	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4002566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4501705	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56955255	0.89[ASN][1000 genomes]
rs58668584	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61495376	0.99[ASN][1000 genomes]
rs62554850	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020331	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032733	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046173	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046193	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729008	0.89[ASN][1000 genomes]
rs72729009	0.89[ASN][1000 genomes]
rs72729010	0.87[ASN][1000 genomes]
rs72729013	0.88[ASN][1000 genomes]
rs72742789	0.81[ASN][1000 genomes]
rs72746350	0.99[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12553524	SYK	Cis_1M	lymphoblastoid	RTeQTL
rs12553524	IPPK	cis	cerebellum	SCAN
rs12553524	SYK	cis	Thyroid	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93564600-93572000	Weak transcription	Lung	lung
2	chr9:93565000-93609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:93565400-93570600	Weak transcription	HMEC	breast
4	chr9:93565400-93570800	Weak transcription	Placenta	Placenta
5	chr9:93565400-93577000	Weak transcription	Colonic Mucosa	Colon
6	chr9:93567000-93572800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:93567400-93570000	Enhancers	Fetal Stomach	stomach
8	chr9:93567600-93571000	Weak transcription	Fetal Intestine Small	intestine
9	chr9:93567600-93573000	Weak transcription	NHEK	skin
10	chr9:93567800-93570800	Weak transcription	Pancreas	Pancrea
11	chr9:93567800-93570800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:93567800-93572000	Weak transcription	Esophagus	oesophagus
13	chr9:93567800-93572000	Weak transcription	K562	blood
14	chr9:93567800-93572400	Weak transcription	Stomach Mucosa	stomach
15	chr9:93567800-93584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:93567800-93584800	Weak transcription	Fetal Intestine Large	intestine
17	chr9:93567800-93597400	Weak transcription	Gastric	stomach
18	chr9:93568000-93569800	Weak transcription	Fetal Kidney	kidney
19	chr9:93568400-93575000	Enhancers	Fetal Thymus	thymus
20	chr9:93568400-93576600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr9:93568600-93573600	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr9:93568800-93569800	Genic enhancers	Monocytes-CD14+_RO01746	blood
23	chr9:93569000-93570200	Genic enhancers	Primary monocytes fromperipheralblood	blood
24	chr9:93569200-93570000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr9:93569200-93570000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr9:93569200-93570200	Flanking Active TSS	Thymus	Thymus
27	chr9:93569200-93570200	Flanking Active TSS	GM12878-XiMat	blood
28	chr9:93569200-93570400	Genic enhancers	Primary B cells from cord blood	blood
29	chr9:93569200-93570400	Genic enhancers	Primary hematopoietic stem cells	blood
30	chr9:93569200-93570600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:93569200-93570800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:93569200-93571200	Enhancers	Spleen	Spleen
33	chr9:93569400-93570000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
34	chr9:93569400-93570400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:93569400-93570400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
36	chr9:93569400-93571400	Enhancers	Primary T cells from cord blood	blood
37	chr9:93569400-93573200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:93569600-93570000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr9:93569600-93570000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:93569600-93570000	Enhancers	Small Intestine	intestine
41	chr9:93569600-93570200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr9:93569600-93570600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr9:93569600-93574600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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