Variant report

Variant	rs12948905
Chromosome Location	chr17:16224875-16224876
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10852834	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11078337	0.83[EUR][1000 genomes]
rs11650283	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11650956	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11651578	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11651955	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653585	0.84[ASN][1000 genomes]
rs11654658	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11655906	0.81[EUR][1000 genomes]
rs11655907	0.81[EUR][1000 genomes]
rs11656811	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11868284	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12150564	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12936529	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12938397	0.82[EUR][1000 genomes]
rs12938878	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12939078	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12945877	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12946717	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476810	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15739	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963811	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2109262	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2324306	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2324307	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35762856	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785620	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3785622	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3785625	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3785626	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4792728	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4792729	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4792731	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4792732	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4792735	0.82[EUR][1000 genomes]
rs56326304	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62074191	0.86[ASN][1000 genomes]
rs62074192	0.86[ASN][1000 genomes]
rs6502498	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7210990	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7224367	0.86[EUR][1000 genomes]
rs8074246	0.86[ASN][1000 genomes]
rs8074727	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9747806	0.89[ASN][1000 genomes]
rs9890539	0.86[EUR][1000 genomes]
rs9890867	0.87[EUR][1000 genomes]
rs9893005	0.82[EUR][1000 genomes]
rs9910148	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9914734	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9944524	0.80[AMR][1000 genomes];0.89[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12948905	ELAC2	cis	parietal	SCAN
rs12948905	PRPSAP2	cis	parietal	SCAN
rs12948905	ZSWIM7	cis	Muscle Skeletal	GTEx
rs12948905	CENPV	cis	Artery Tibial	GTEx
rs12948905	CENPV	cis	parietal	SCAN
rs12948905	CENPV	cis	lymphoblastoid	seeQTL
rs12948905	ADORA2B	cis	Muscle Skeletal	GTEx
rs12948905	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs12948905	ADORA2B	cis	Artery Tibial	GTEx
rs12948905	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs12948905	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs12948905	PRR6	cis	multi-tissue	Pritchard
rs12948905	TRPV2	cis	cerebellum	SCAN
rs12948905	TRPV2	cis	parietal	SCAN

Chromatin state (count:116 , 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	chr17:16216400-16231000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr17:16216800-16228800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr17:16216800-16228800	Weak transcription	GM12878-XiMat	blood
36	chr17:16216800-16229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr17:16216800-16232400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr17:16217000-16226000	Weak transcription	NH-A	brain
39	chr17:16217000-16232400	Weak transcription	Gastric	stomach
40	chr17:16217000-16246000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr17:16217200-16226000	Weak transcription	Fetal Thymus	thymus
42	chr17:16217200-16228200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:16217200-16228800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr17:16217200-16228800	Weak transcription	Pancreas	Pancrea
45	chr17:16217200-16228800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr17:16217200-16255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr17:16217400-16225000	Weak transcription	Fetal Lung	lung
48	chr17:16217400-16226000	Weak transcription	Fetal Kidney	kidney
49	chr17:16217400-16229000	Weak transcription	Brain Hippocampus Middle	brain
50	chr17:16217400-16232400	Weak transcription	A549	lung

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