Variant report

Variant	rs56326304
Chromosome Location	chr17:16223335-16223336
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10852834	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11078337	0.84[EUR][1000 genomes]
rs11650283	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11650956	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11651578	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11651955	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653585	0.84[ASN][1000 genomes]
rs11654658	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11655906	0.80[EUR][1000 genomes]
rs11655907	0.80[EUR][1000 genomes]
rs11656811	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11868284	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12150564	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12936529	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12938397	0.83[EUR][1000 genomes]
rs12938878	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12939078	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12945877	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12946717	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12948905	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476810	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15739	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963811	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2109262	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2324306	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2324307	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35762856	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785620	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3785622	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3785625	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3785626	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4792728	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4792729	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4792731	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4792732	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4792735	0.81[EUR][1000 genomes]
rs62074191	0.86[ASN][1000 genomes]
rs62074192	0.86[ASN][1000 genomes]
rs6502498	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7210990	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7224367	0.87[EUR][1000 genomes]
rs8074246	0.86[ASN][1000 genomes]
rs8074727	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9747806	0.89[ASN][1000 genomes]
rs9890539	0.87[EUR][1000 genomes]
rs9890867	0.86[EUR][1000 genomes]
rs9893005	0.81[EUR][1000 genomes]
rs9910148	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9914734	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9944524	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv907717	chr17:16076898-16239832	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
6	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs56326304	ADORA2B	cis	Muscle Skeletal	GTEx
rs56326304	ADORA2B	cis	Artery Tibial	GTEx
rs56326304	ZSWIM7	cis	Muscle Skeletal	GTEx
rs56326304	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs56326304	PRR6	cis	multi-tissue	Pritchard
rs56326304	CENPV	cis	Artery Tibial	GTEx
rs56326304	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs56326304	NCOR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16190600-16229600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr17:16191400-16226000	Weak transcription	HSMMtube	muscle
3	chr17:16192800-16229000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr17:16197800-16230000	Weak transcription	Brain Angular Gyrus	brain
5	chr17:16200800-16228200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr17:16201000-16232400	Weak transcription	Hela-S3	cervix
7	chr17:16201600-16228800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr17:16201600-16246400	Weak transcription	Fetal Brain Male	brain
9	chr17:16203600-16228800	Weak transcription	Primary B cells from cord blood	blood
10	chr17:16204200-16228800	Weak transcription	Brain Substantia Nigra	brain
11	chr17:16204600-16226000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:16205400-16228800	Weak transcription	Colon Smooth Muscle	Colon
13	chr17:16205800-16226000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr17:16205800-16228800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr17:16205800-16228800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr17:16205800-16229000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:16205800-16229000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr17:16205800-16245600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr17:16206000-16232200	Weak transcription	HMEC	breast
20	chr17:16206000-16245800	Weak transcription	Brain Anterior Caudate	brain
21	chr17:16206000-16246000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr17:16206200-16228800	Weak transcription	Esophagus	oesophagus
23	chr17:16207400-16232400	Weak transcription	Right Atrium	heart
24	chr17:16209000-16245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr17:16214400-16228200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:16214400-16228600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr17:16214600-16225800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr17:16214600-16228800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr17:16214600-16229000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr17:16214600-16233000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr17:16214600-16255200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr17:16215800-16228800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr17:16216400-16223400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr17:16216400-16231000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr17:16216800-16223400	Strong transcription	Fetal Muscle Leg	muscle
36	chr17:16216800-16228800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr17:16216800-16228800	Weak transcription	GM12878-XiMat	blood
38	chr17:16216800-16229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:16216800-16232400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr17:16217000-16223400	Strong transcription	Primary T cells from cord blood	blood
41	chr17:16217000-16226000	Weak transcription	NH-A	brain
42	chr17:16217000-16232400	Weak transcription	Gastric	stomach
43	chr17:16217000-16246000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr17:16217200-16226000	Weak transcription	Fetal Thymus	thymus
45	chr17:16217200-16228200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:16217200-16228800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr17:16217200-16228800	Weak transcription	Pancreas	Pancrea
48	chr17:16217200-16228800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr17:16217200-16255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr17:16217400-16225000	Weak transcription	Fetal Lung	lung

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