Variant report

Variant	rs7259272
Chromosome Location	chr19:38183115-38183116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF781-2	chr19:38183053-38183164	NONHSAT066149
2	lnc-ZNF781-2	chr19:38183053-38183164	NONHSAT066150
3	lnc-ZNF781-2	chr19:38183053-38183216	NONHSAT066152
4	lnc-ZNF781-2	chr19:38183053-38183134	NONHSAT066153

Extended variants
information (count: 48 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10153500	0.88[CHB][hapmap];0.95[CHD][hapmap]
rs10445548	0.82[EUR][1000 genomes]
rs1061753	0.80[EUR][1000 genomes]
rs11880056	0.88[CHB][hapmap]
rs11883255	0.88[CHB][hapmap]
rs17244713	0.92[CEU][hapmap]
rs17244769	0.91[CEU][hapmap]
rs17246792	0.81[YRI][hapmap]
rs17303902	0.92[CEU][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs17304703	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs17305193	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17305228	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17305823	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs17306900	0.85[CEU][hapmap]
rs1871196	0.82[EUR][1000 genomes]
rs2058852	0.96[ASN][1000 genomes]
rs2291001	0.92[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2306201	0.92[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2385005	0.88[CEU][hapmap]
rs35153242	0.92[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs55681348	0.83[EUR][1000 genomes]
rs55718806	0.81[EUR][1000 genomes]
rs55743020	0.84[EUR][1000 genomes]
rs55754546	0.80[EUR][1000 genomes]
rs55865869	0.82[EUR][1000 genomes]
rs55909413	0.82[EUR][1000 genomes]
rs56077756	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57654288	0.82[EUR][1000 genomes]
rs62108291	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62108306	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245855	0.85[CEU][hapmap]
rs7245981	0.88[CHB][hapmap]
rs7253081	0.81[YRI][hapmap]
rs7255313	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73031330	0.80[EUR][1000 genomes]
rs73033122	0.82[EUR][1000 genomes]
rs73033134	0.81[EUR][1000 genomes]
rs73033142	0.81[EUR][1000 genomes]
rs73035159	0.82[EUR][1000 genomes]
rs73035160	0.83[EUR][1000 genomes]
rs8101610	0.92[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs8101991	0.86[CHB][hapmap]
rs8104282	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs8104994	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs8108268	0.81[EUR][1000 genomes]
rs8111790	0.92[CEU][hapmap];0.82[EUR][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7259272	AC012309.5	cis	Esophagus Muscularis	GTEx
rs7259272	ZNF781	cis	Thyroid	GTEx
rs7259272	PVR	cis	parietal	SCAN
rs7259272	AC012309.5	cis	Muscle Skeletal	GTEx
rs7259272	AC012309.5	cis	Heart Left Ventricle	GTEx
rs7259272	HKR1	cis	Whole Blood	GTEx
rs7259272	CCDC97	cis	cerebellum	SCAN
rs7259272	POU2F2	cis	parietal	SCAN
rs7259272	AC012309.5	cis	Esophagus Mucosa	GTEx
rs7259272	ZNF781	trans	cerebellum	SCAN
rs7259272	AC012309.5	cis	Artery Tibial	GTEx
rs7259272	AC012309.5	cis	Thyroid	GTEx
rs7259272	DMPK	cis	parietal	SCAN
rs7259272	PLEKHG2	cis	cerebellum	SCAN
rs7259272	C19orf61	cis	cerebellum	SCAN
rs7259272	CEACAM3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38181200-38183600	Active TSS	Brain Germinal Matrix	brain
2	chr19:38182000-38183600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr19:38182200-38183400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr19:38182200-38183600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:38182200-38183600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:38182200-38183600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:38182200-38183600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:38182200-38183600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr19:38182200-38183600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:38182200-38183600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:38182200-38183600	Active TSS	Colon Smooth Muscle	Colon
12	chr19:38182200-38183600	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr19:38182200-38183600	Active TSS	Fetal Kidney	kidney
14	chr19:38182200-38183600	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr19:38182200-38183600	Active TSS	Psoas Muscle	Psoas
16	chr19:38182200-38183600	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr19:38182200-38183600	Active TSS	Stomach Smooth Muscle	stomach
18	chr19:38182200-38183600	Active TSS	HepG2	liver
19	chr19:38182200-38183600	Active TSS	NHDF-Ad	bronchial
20	chr19:38182200-38183600	Active TSS	NHLF	lung
21	chr19:38182200-38183600	Active TSS	Osteobl	bone
22	chr19:38182200-38184000	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr19:38182200-38184200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:38182200-38184200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38182200-38184200	Active TSS	Duodenum Mucosa	Duodenum
26	chr19:38182200-38184200	Flanking Active TSS	Dnd41	blood
27	chr19:38182200-38184400	Active TSS	Brain Hippocampus Middle	brain
28	chr19:38182400-38183200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr19:38182400-38183600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:38182400-38183600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
31	chr19:38182400-38183600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
32	chr19:38182400-38183600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:38182400-38183600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr19:38182400-38183600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr19:38182400-38183600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr19:38182400-38183600	Active TSS	Muscle Satellite Cultured Cells	--
37	chr19:38182400-38183600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:38182400-38183600	Active TSS	Aorta	Aorta
39	chr19:38182400-38183600	Active TSS	Fetal Intestine Small	intestine
40	chr19:38182400-38183600	Active TSS	Fetal Muscle Leg	muscle
41	chr19:38182400-38183600	Active TSS	Fetal Stomach	stomach
42	chr19:38182400-38183600	Active TSS	Ovary	ovary
43	chr19:38182400-38183600	Active TSS	Rectal Smooth Muscle	rectum
44	chr19:38182400-38183600	ZNF genes & repeats	GM12878-XiMat	blood
45	chr19:38182400-38183600	Active TSS	NH-A	brain
46	chr19:38182400-38183800	Active TSS	Fetal Muscle Trunk	muscle
47	chr19:38182400-38184000	Active TSS	Fetal Lung	lung
48	chr19:38182400-38184200	Active TSS	Brain Angular Gyrus	brain
49	chr19:38182400-38184200	Active TSS	Fetal Brain Male	brain
50	chr19:38182400-38184400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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