Variant report

Variant	rs17363566
Chromosome Location	chr13:50934892-50934893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50929110..50931942-chr13:50932169..50935113,3	MCF-7	breast:
2	chr13:50698526..50701372-chr13:50933812..50935948,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11842790	1.00[ASN][1000 genomes]
rs12853498	1.00[ASN][1000 genomes]
rs12855386	1.00[ASN][1000 genomes]
rs12864797	0.95[AFR][1000 genomes]
rs12867018	1.00[ASN][1000 genomes]
rs12871645	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874827	1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs12876227	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17074093	1.00[ASN][1000 genomes]
rs17074141	1.00[ASN][1000 genomes]
rs17074143	1.00[ASN][1000 genomes]
rs17074145	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17363026	1.00[ASN][1000 genomes]
rs2066664	1.00[ASN][1000 genomes]
rs2066673	1.00[ASN][1000 genomes]
rs2066679	1.00[ASN][1000 genomes]
rs3095158	0.87[ASN][1000 genomes]
rs3095160	0.87[ASN][1000 genomes]
rs3095164	0.87[ASN][1000 genomes]
rs3095165	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3116594	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs3116595	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3118648	0.87[ASN][1000 genomes]
rs3118649	0.87[ASN][1000 genomes]
rs3118650	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34042295	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34357487	1.00[ASN][1000 genomes]
rs34374535	1.00[ASN][1000 genomes]
rs34453016	1.00[ASN][1000 genomes]
rs34556868	1.00[ASN][1000 genomes]
rs34700115	1.00[ASN][1000 genomes]
rs34712361	1.00[ASN][1000 genomes]
rs34972893	1.00[ASN][1000 genomes]
rs35299189	1.00[ASN][1000 genomes]
rs35383320	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35413012	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35542898	1.00[ASN][1000 genomes]
rs35650342	1.00[ASN][1000 genomes]
rs35902227	1.00[ASN][1000 genomes]
rs35980102	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67217502	1.00[ASN][1000 genomes]
rs67964536	1.00[ASN][1000 genomes]
rs706603	1.00[ASN][1000 genomes]
rs71428294	1.00[ASN][1000 genomes]
rs71436217	1.00[ASN][1000 genomes]
rs71436218	1.00[ASN][1000 genomes]
rs71436219	1.00[ASN][1000 genomes]
rs71436220	1.00[ASN][1000 genomes]
rs71436222	1.00[ASN][1000 genomes]
rs73498084	0.81[AFR][1000 genomes]
rs73500218	0.90[AFR][1000 genomes]
rs7986582	0.86[ASN][1000 genomes]
rs7990202	1.00[ASN][1000 genomes]
rs806315	1.00[ASN][1000 genomes]
rs806318	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17363566	AGPAT4	trans	brain	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50930000-50935800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr13:50930200-50939200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr13:50930200-50939600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr13:50930800-50935000	Enhancers	Fetal Thymus	thymus
5	chr13:50931600-50939000	Weak transcription	HepG2	liver
6	chr13:50932000-50940800	Weak transcription	Small Intestine	intestine
7	chr13:50932400-50936200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr13:50932400-50936200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr13:50932400-50936400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr13:50932800-50935800	Weak transcription	Spleen	Spleen
11	chr13:50932800-50936200	Weak transcription	Fetal Brain Female	brain
12	chr13:50932800-50939400	Weak transcription	Gastric	stomach
13	chr13:50932800-50939400	Weak transcription	Pancreas	Pancrea
14	chr13:50932800-50939600	Weak transcription	Fetal Kidney	kidney
15	chr13:50933000-50935200	Weak transcription	Liver	Liver
16	chr13:50933000-50935200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr13:50933000-50935800	Weak transcription	Fetal Muscle Leg	muscle
18	chr13:50933000-50935800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr13:50933000-50936000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:50933200-50936600	Weak transcription	Fetal Heart	heart
21	chr13:50933200-50939200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr13:50933400-50935200	Weak transcription	Brain Anterior Caudate	brain
23	chr13:50933400-50939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr13:50933400-50944600	Weak transcription	Fetal Lung	lung
25	chr13:50933800-50944000	Weak transcription	Primary B cells from cord blood	blood
26	chr13:50934000-50935000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr13:50934000-50935600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr13:50934000-50939600	Weak transcription	Brain Germinal Matrix	brain
29	chr13:50934200-50935000	Enhancers	Lung	lung
30	chr13:50934200-50935400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr13:50934200-50935800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr13:50934400-50935000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:50934600-50936000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr13:50934600-50942000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr13:50934800-50935400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr13:50934800-50935800	Enhancers	Dnd41	blood

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