Variant report

Variant	rs2047679
Chromosome Location	chr15:82531881-82531882
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11073036	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11630197	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11631813	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs11633000	0.89[ASN][1000 genomes]
rs11639440	0.93[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap]
rs11854157	0.83[YRI][hapmap]
rs11854289	1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11854483	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12324875	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1501367	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1566559	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1566560	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1566561	0.83[ASN][1000 genomes]
rs16973457	1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1846908	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1948741	0.88[ASN][1000 genomes]
rs1948742	0.81[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1972460	0.87[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2016372	0.84[ASN][1000 genomes]
rs2134046	0.96[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2457497	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2665103	0.93[CHB][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs28454949	0.97[ASN][1000 genomes]
rs28522807	0.93[ASN][1000 genomes]
rs28564699	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28610286	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3759800	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[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]
rs3858953	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3902959	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238534	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4267268	0.82[ASN][1000 genomes]
rs4296215	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4778674	0.91[ASN][1000 genomes]
rs4778986	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4778987	0.87[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4778990	0.91[ASN][1000 genomes]
rs56398167	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61554133	0.83[ASN][1000 genomes]
rs62012054	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62012055	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7167504	0.89[ASN][1000 genomes]
rs7176926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72749557	0.81[ASN][1000 genomes]
rs72749560	0.81[ASN][1000 genomes]
rs72749561	0.81[ASN][1000 genomes]
rs72749564	0.82[ASN][1000 genomes]
rs72749575	0.84[ASN][1000 genomes]
rs72749586	0.84[ASN][1000 genomes]
rs7403041	0.91[ASN][1000 genomes]
rs7403244	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs8025964	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8027301	0.81[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs8027661	0.81[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs8030210	0.88[ASN][1000 genomes]
rs8030250	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8032633	0.88[ASN][1000 genomes]
rs8033313	0.87[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs905450	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9972440	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
7	esv1801737	chr15:82468455-82589044	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv570246	chr15:82485707-82581264	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1041506	chr15:82496164-82581427	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv1798145	chr15:82506790-82581264	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv904440	chr15:82524544-82591082	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2047679	AP3B2	cis	cerebellum	SCAN
rs2047679	AP3B2	cis	parietal	SCAN
rs2047679	RP13-608F4.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82432600-82552800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:82481800-82553000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:82496200-82532000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:82496400-82532000	Weak transcription	Fetal Brain Male	brain
5	chr15:82497000-82553600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:82497600-82536000	Weak transcription	Fetal Heart	heart
7	chr15:82499000-82550800	Weak transcription	HUVEC	blood vessel
8	chr15:82499400-82553000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:82501400-82532000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:82501800-82544600	Weak transcription	Brain Angular Gyrus	brain
11	chr15:82503000-82542200	Weak transcription	Stomach Mucosa	stomach
12	chr15:82503200-82552800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:82503600-82553000	Weak transcription	Small Intestine	intestine
14	chr15:82503800-82553200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:82504200-82553200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:82507400-82553000	Weak transcription	NH-A	brain
17	chr15:82508200-82553800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:82510600-82532600	Weak transcription	Ovary	ovary
19	chr15:82510800-82554200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:82511800-82534800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:82511800-82554200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:82512600-82539600	Weak transcription	Spleen	Spleen
23	chr15:82515800-82553600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:82519800-82532600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:82520000-82553000	Weak transcription	Gastric	stomach
26	chr15:82520000-82553000	Weak transcription	Right Ventricle	heart
27	chr15:82520000-82553400	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:82520000-82554200	Weak transcription	Pancreas	Pancrea
29	chr15:82520200-82532000	Weak transcription	Fetal Brain Female	brain
30	chr15:82520200-82533000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:82520200-82553000	Weak transcription	Psoas Muscle	Psoas
32	chr15:82520200-82554400	Weak transcription	Esophagus	oesophagus
33	chr15:82520400-82532000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:82521400-82532000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:82523000-82550000	Weak transcription	Brain Anterior Caudate	brain
36	chr15:82523400-82532000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:82523400-82532000	Weak transcription	Osteobl	bone
38	chr15:82523600-82553400	Weak transcription	Fetal Kidney	kidney
39	chr15:82524000-82545400	Weak transcription	Fetal Intestine Small	intestine
40	chr15:82524200-82532000	Weak transcription	Hela-S3	cervix
41	chr15:82524800-82552600	Weak transcription	K562	blood
42	chr15:82527800-82534400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr15:82528600-82532400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:82528600-82533400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:82528600-82534000	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:82528800-82533400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:82528800-82533800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:82529200-82533800	Strong transcription	Thymus	Thymus
49	chr15:82529600-82533000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr15:82529600-82533400	Strong transcription	Adipose Nuclei	Adipose

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