Variant report

Variant	rs17269819
Chromosome Location	chr15:82467001-82467002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr15:82466877-82467248	SH-SY5Y	brain:	n/a	chr15:82466976-82466983 chr15:82466970-82466982
2	SPI1	chr15:82466852-82467107	GM12878	blood:	n/a	n/a
3	GATA3	chr15:82466741-82467401	SK-N-SH	brain:	n/a	chr15:82466976-82466983 chr15:82466970-82466982
4	RUNX3	chr15:82466493-82467091	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNU1-77P	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11548681	0.90[ASN][1000 genomes]
rs16973456	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs17354185	0.81[EUR][1000 genomes]
rs28542747	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587326	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28689861	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28694364	0.83[EUR][1000 genomes]
rs35462466	0.90[ASN][1000 genomes]
rs4778665	0.83[EUR][1000 genomes]
rs4778979	0.90[ASN][1000 genomes]
rs4778984	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4778989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62011975	0.88[EUR][1000 genomes]
rs62012003	0.88[EUR][1000 genomes]
rs62012004	0.88[EUR][1000 genomes]
rs62012046	0.81[EUR][1000 genomes]
rs62012047	0.81[EUR][1000 genomes]
rs62012049	0.81[EUR][1000 genomes]
rs7165536	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168667	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs8034801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042461	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs9944185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457212	chr15:82454283-82573255	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking 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
2	nsv570243	chr15:82454283-82573255	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv457213	chr15:82456227-82573255	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv570244	chr15:82456227-82573255	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv570245	chr15:82456227-82591082	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1041040	chr15:82465124-82606410	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17269819	AP3B2	cis	Artery Tibial	GTEx
rs17269819	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs17269819	AP3B2	cis	Nerve Tibial	GTEx
rs17269819	AP3B2	cis	Muscle Skeletal	GTEx
rs17269819	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs17269819	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs17269819	RP11-152F13.3	cis	lung	GTEx
rs17269819	AP3B2	cis	lung	GTEx
rs17269819	AP3B2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82419200-82470600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:82432600-82476400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:82432600-82552800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:82441400-82469600	Weak transcription	Fetal Brain Male	brain
5	chr15:82444600-82495800	Weak transcription	Fetal Intestine Small	intestine
6	chr15:82451000-82469800	Weak transcription	Psoas Muscle	Psoas
7	chr15:82452600-82470600	Weak transcription	Esophagus	oesophagus
8	chr15:82455400-82475200	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:82455400-82475200	Weak transcription	Pancreas	Pancrea
10	chr15:82455600-82469200	Weak transcription	Brain Anterior Caudate	brain
11	chr15:82455600-82475200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:82455800-82467200	Weak transcription	Spleen	Spleen
13	chr15:82455800-82469800	Weak transcription	Ovary	ovary
14	chr15:82456000-82469800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:82456000-82475800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:82456000-82475800	Weak transcription	Lung	lung
17	chr15:82456000-82510000	Weak transcription	Thymus	Thymus
18	chr15:82456200-82469000	Weak transcription	Osteobl	bone
19	chr15:82456200-82469600	Weak transcription	HSMMtube	muscle
20	chr15:82456200-82470000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:82456200-82475200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:82456200-82475600	Weak transcription	Fetal Brain Female	brain
23	chr15:82456400-82469400	Weak transcription	HSMM	muscle
24	chr15:82456400-82470600	Weak transcription	Left Ventricle	heart
25	chr15:82456400-82473000	Weak transcription	Fetal Intestine Large	intestine
26	chr15:82456400-82474200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:82456400-82475200	Weak transcription	Fetal Muscle Leg	muscle
28	chr15:82456400-82475200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr15:82456400-82475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr15:82456400-82475800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr15:82456400-82480600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:82456400-82487000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr15:82456400-82502200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr15:82456400-82502400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:82456400-82502600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr15:82456400-82502800	Weak transcription	Gastric	stomach
37	chr15:82456400-82505400	Weak transcription	Dnd41	blood
38	chr15:82456400-82505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr15:82456400-82505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:82456600-82474200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr15:82456600-82474400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:82456600-82474400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:82456600-82478600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:82456600-82497400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:82456800-82475200	Weak transcription	Liver	Liver
46	chr15:82456800-82509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr15:82457000-82469800	Weak transcription	Aorta	Aorta
48	chr15:82458200-82504800	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:82458600-82475600	Weak transcription	GM12878-XiMat	blood
50	chr15:82458600-82479200	Weak transcription	Primary hematopoietic stem cells	blood

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