Variant report

Variant	rs12938878
Chromosome Location	chr17:16216605-16216606
allele	A/C
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	RUNX3	chr17:16216574-16216977	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:16216588-16217193	HepG2	liver:	n/a	n/a
3	TBP	chr17:16216547-16217236	HepG2	liver:	n/a	n/a
4	MYBL2	chr17:16216571-16217227	HepG2	liver:	n/a	n/a
5	MAX	chr17:16216339-16217337	HepG2	liver:	n/a	n/a
6	YY1	chr17:16216500-16216922	HepG2	liver:	n/a	n/a
7	CUX1	chr17:16216578-16217222	K562	blood:	n/a	n/a
8	FOXA1	chr17:16216560-16217217	HepG2	liver:	n/a	chr17:16216962-16216974
9	MYBL2	chr17:16216448-16217268	HepG2	liver:	n/a	n/a
10	SP1	chr17:16216593-16217242	HepG2	liver:	n/a	n/a
11	HEY1	chr17:16216549-16217295	HepG2	liver:	n/a	n/a
12	HEY1	chr17:16216521-16217202	HepG2	liver:	n/a	n/a
13	ARID3A	chr17:16216538-16217220	HepG2	liver:	n/a	n/a
14	TEAD4	chr17:16216559-16217281	K562	blood:	n/a	n/a
15	KAP1	chr17:16216593-16217249	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
PIGL	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1029809	0.85[EUR][1000 genomes]
rs10852834	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11078337	0.91[EUR][1000 genomes]
rs11650283	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11650427	0.85[EUR][1000 genomes]
rs11650956	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651578	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651955	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11653650	0.84[EUR][1000 genomes]
rs11654658	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655325	0.87[EUR][1000 genomes]
rs11656811	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868284	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150564	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12936233	0.82[EUR][1000 genomes]
rs12936529	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12938394	0.81[EUR][1000 genomes]
rs12938397	0.91[EUR][1000 genomes]
rs12939078	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12945855	0.82[EUR][1000 genomes]
rs12945877	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12946717	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12948244	0.83[EUR][1000 genomes]
rs12948905	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1476810	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs15739	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1963811	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014604	0.83[EUR][1000 genomes]
rs2109262	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2324306	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2324307	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28516015	0.83[EUR][1000 genomes]
rs3095171	0.83[EUR][1000 genomes]
rs3112511	0.83[EUR][1000 genomes]
rs3112513	0.83[EUR][1000 genomes]
rs35762856	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3785620	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3785621	0.87[EUR][1000 genomes]
rs3785622	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785623	0.84[EUR][1000 genomes]
rs3785625	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3785626	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791665	0.84[EUR][1000 genomes]
rs4792728	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4792729	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4792730	0.83[EUR][1000 genomes]
rs4792731	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4792732	0.88[ASN][1000 genomes]
rs56326304	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62072528	0.84[EUR][1000 genomes]
rs6502498	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6502499	0.84[EUR][1000 genomes]
rs7210990	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7215071	0.84[EUR][1000 genomes]
rs7219687	0.83[EUR][1000 genomes]
rs7225920	0.84[EUR][1000 genomes]
rs8074727	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9747114	0.83[EUR][1000 genomes]
rs9909022	0.84[EUR][1000 genomes]
rs9910148	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9914734	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9916220	0.84[EUR][1000 genomes]
rs9944524	0.92[AMR][1000 genomes];0.98[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	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12938878	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs12938878	ADORA2B	cis	Muscle Skeletal	GTEx
rs12938878	ADORA2B	cis	Thyroid	GTEx
rs12938878	CENPV	cis	Artery Tibial	GTEx
rs12938878	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs12938878	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs12938878	PRR6	cis	multi-tissue	Pritchard
rs12938878	ZSWIM7	cis	Muscle Skeletal	GTEx
rs12938878	ADORA2B	cis	Artery Tibial	GTEx

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	chr17:16190800-16220800	Weak transcription	Aorta	Aorta
3	chr17:16191400-16218400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:16191400-16219400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr17:16191400-16226000	Weak transcription	HSMMtube	muscle
6	chr17:16191600-16216800	Weak transcription	Fetal Kidney	kidney
7	chr17:16191800-16217200	Weak transcription	HSMM	muscle
8	chr17:16192800-16229000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr17:16197800-16230000	Weak transcription	Brain Angular Gyrus	brain
10	chr17:16198400-16220400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr17:16200800-16228200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr17:16201000-16232400	Weak transcription	Hela-S3	cervix
13	chr17:16201200-16223200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr17:16201600-16228800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr17:16201600-16246400	Weak transcription	Fetal Brain Male	brain
16	chr17:16201800-16221000	Weak transcription	Colonic Mucosa	Colon
17	chr17:16203600-16228800	Weak transcription	Primary B cells from cord blood	blood
18	chr17:16204000-16219400	Weak transcription	Brain Germinal Matrix	brain
19	chr17:16204200-16220000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr17:16204200-16228800	Weak transcription	Brain Substantia Nigra	brain
21	chr17:16204600-16226000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:16205400-16228800	Weak transcription	Colon Smooth Muscle	Colon
23	chr17:16205800-16218400	Weak transcription	Right Ventricle	heart
24	chr17:16205800-16220600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr17:16205800-16226000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr17:16205800-16228800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr17:16205800-16228800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr17:16205800-16229000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:16205800-16229000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr17:16205800-16245600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:16206000-16216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr17:16206000-16219800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:16206000-16219800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr17:16206000-16220400	Weak transcription	NHEK	skin
35	chr17:16206000-16232200	Weak transcription	HMEC	breast
36	chr17:16206000-16245800	Weak transcription	Brain Anterior Caudate	brain
37	chr17:16206000-16246000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr17:16206200-16219800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:16206200-16228800	Weak transcription	Esophagus	oesophagus
40	chr17:16206600-16216800	Weak transcription	NHLF	lung
41	chr17:16206600-16217000	Weak transcription	Brain Hippocampus Middle	brain
42	chr17:16206800-16218000	Weak transcription	Ovary	ovary
43	chr17:16206800-16219400	Weak transcription	Placenta	Placenta
44	chr17:16207400-16232400	Weak transcription	Right Atrium	heart
45	chr17:16208000-16221000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr17:16209000-16245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr17:16210800-16216800	Weak transcription	Fetal Muscle Leg	muscle
48	chr17:16210800-16219400	Weak transcription	Lung	lung
49	chr17:16210800-16219600	Weak transcription	Osteobl	bone
50	chr17:16211000-16216800	Weak transcription	Adipose Nuclei	Adipose

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