Variant report

Variant	rs6505489
Chromosome Location	chr17:34024784-34024785
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	chr17:34024050..34027708-chr17:34038047..34041626,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1049379	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12150359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949341	0.85[ASN][1000 genomes]
rs1476553	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs161182	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161183	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161184	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1634684	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs170483	0.84[ASN][1000 genomes]
rs178649	0.85[EUR][1000 genomes]
rs225245	0.81[EUR][1000 genomes]
rs225255	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs225269	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225272	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225273	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225281	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs225282	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs225284	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225290	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225293	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225297	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225299	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225302	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs226085	0.83[ASN][1000 genomes]
rs226086	0.85[ASN][1000 genomes]
rs226088	0.85[ASN][1000 genomes]
rs226428	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226432	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs226434	0.84[ASN][1000 genomes]
rs226439	0.84[ASN][1000 genomes]
rs226441	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285742	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301730	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs321599	0.86[EUR][1000 genomes]
rs321601	0.81[EUR][1000 genomes]
rs321617	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs321618	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3890901	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795085	0.86[EUR][1000 genomes]
rs4796103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505490	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505491	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505492	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505493	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67296463	0.83[ASN][1000 genomes]
rs71366475	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs720774	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7217565	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7221081	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7221096	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7406966	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8064556	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8067294	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8073375	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8078905	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9635770	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6505489	AP2B1	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:33975000-34025800	Strong transcription	Primary B cells from peripheral blood	blood
4	chr17:33992800-34028200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr17:33999400-34043400	Weak transcription	Fetal Brain Male	brain
6	chr17:34002000-34032200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr17:34002000-34036800	Weak transcription	Colonic Mucosa	Colon
8	chr17:34005400-34028400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr17:34005800-34026600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr17:34006600-34032800	Weak transcription	Stomach Mucosa	stomach
11	chr17:34006600-34039800	Weak transcription	Small Intestine	intestine
12	chr17:34011000-34026600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr17:34011800-34036200	Weak transcription	Hela-S3	cervix
14	chr17:34013600-34036000	Weak transcription	NHLF	lung
15	chr17:34014600-34024800	Strong transcription	Primary B cells from cord blood	blood
16	chr17:34016000-34036600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr17:34017200-34034600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr17:34017800-34040400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:34018800-34034600	Weak transcription	Pancreas	Pancrea
20	chr17:34018800-34036000	Weak transcription	Gastric	stomach
21	chr17:34018800-34050600	Weak transcription	Esophagus	oesophagus
22	chr17:34019000-34044000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr17:34020800-34024800	Strong transcription	Lung	lung
24	chr17:34021000-34036800	Weak transcription	NHEK	skin
25	chr17:34021200-34025800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr17:34021200-34037000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr17:34022000-34036000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:34022000-34036200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:34022200-34036000	Weak transcription	Ovary	ovary
30	chr17:34022200-34042400	Weak transcription	Aorta	Aorta
31	chr17:34022400-34036000	Weak transcription	Left Ventricle	heart
32	chr17:34022600-34035400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr17:34022600-34036000	Weak transcription	Psoas Muscle	Psoas
34	chr17:34022800-34036000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:34022800-34036200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:34022800-34036400	Weak transcription	Colon Smooth Muscle	Colon
37	chr17:34023000-34034800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr17:34023000-34034800	Weak transcription	Brain Angular Gyrus	brain
39	chr17:34023000-34035200	Weak transcription	GM12878-XiMat	blood
40	chr17:34023000-34036800	Weak transcription	NHDF-Ad	bronchial
41	chr17:34023200-34026000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr17:34023200-34028600	Weak transcription	Right Atrium	heart
43	chr17:34023200-34031200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr17:34023200-34034600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr17:34023200-34034800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr17:34023200-34034800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr17:34023200-34035000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr17:34023200-34035800	Weak transcription	Brain Anterior Caudate	brain
49	chr17:34023200-34036000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr17:34023200-34036000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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