Variant report

Variant	rs8110293
Chromosome Location	chr19:38313102-38313103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIPA1L3-3	chr19:38310864-38314365	NONHSAT066169

Extended variants
information (count: 49 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1048505	0.91[ASN][1000 genomes]
rs12150862	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151082	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.91[ASN][1000 genomes]
rs1643455	1.00[CHB][hapmap]
rs1643459	1.00[CHB][hapmap]
rs17248097	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17248670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249138	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249336	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs17305823	1.00[JPT][hapmap]
rs17306900	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs35153242	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs3859549	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614853	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55681348	0.86[ASN][1000 genomes]
rs55743020	0.91[ASN][1000 genomes]
rs55752822	0.81[EUR][1000 genomes]
rs55813548	0.82[EUR][1000 genomes]
rs55974157	0.82[EUR][1000 genomes]
rs55983118	0.81[EUR][1000 genomes]
rs56184201	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56207124	0.81[EUR][1000 genomes]
rs56230664	0.81[EUR][1000 genomes]
rs56233644	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246446	0.81[EUR][1000 genomes]
rs56268127	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56290614	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56351266	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56676595	0.82[EUR][1000 genomes]
rs6508755	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs705501	1.00[CHB][hapmap]
rs7245855	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73027472	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73027480	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73039029	0.91[ASN][1000 genomes]
rs73041006	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73041036	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7343065	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8100199	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs833905	1.00[CHB][hapmap]
rs833919	1.00[CHB][hapmap]
rs833920	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs8110293	ARHGEF1	cis	cerebellum	SCAN
rs8110293	PHLDB3	cis	cerebellum	SCAN
rs8110293	AC012309.5	cis	Thyroid	GTEx
rs8110293	AC012309.5	cis	Heart Left Ventricle	GTEx
rs8110293	ZNF781	cis	Thyroid	GTEx
rs8110293	AC012309.5	cis	Esophagus Muscularis	GTEx
rs8110293	AC012309.5	cis	Esophagus Mucosa	GTEx
rs8110293	TRAPPC6A	cis	cerebellum	SCAN
rs8110293	C19orf61	cis	cerebellum	SCAN
rs8110293	ZNF226	cis	cerebellum	SCAN
rs8110293	PLEKHG2	cis	cerebellum	SCAN
rs8110293	AC012309.5	cis	Artery Tibial	GTEx
rs8110293	HKR1	cis	multi-tissue	Pritchard
rs8110293	AC012309.5	cis	Muscle Skeletal	GTEx
rs8110293	KIAA0961	cis	multi-tissue	Pritchard

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38308600-38314800	Weak transcription	Gastric	stomach
2	chr19:38308800-38313200	Weak transcription	Esophagus	oesophagus
3	chr19:38308800-38314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:38308800-38314400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:38308800-38314400	Weak transcription	Brain Angular Gyrus	brain
6	chr19:38308800-38314400	Weak transcription	Fetal Muscle Leg	muscle
7	chr19:38308800-38314400	Weak transcription	Right Ventricle	heart
8	chr19:38308800-38314600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:38308800-38314600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr19:38308800-38314600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:38308800-38315400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:38309000-38313200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:38309000-38314200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:38309000-38314200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:38309000-38314600	Weak transcription	Fetal Heart	heart
16	chr19:38309000-38316800	Weak transcription	Stomach Mucosa	stomach
17	chr19:38309400-38315000	Weak transcription	Placenta	Placenta
18	chr19:38309600-38314800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:38309600-38319200	ZNF genes & repeats	Fetal Brain Female	brain
20	chr19:38310000-38317000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr19:38310000-38317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:38310000-38318200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:38310200-38313800	ZNF genes & repeats	Fetal Brain Male	brain
24	chr19:38310200-38317600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr19:38310600-38315000	Weak transcription	Pancreas	Pancrea
26	chr19:38310800-38313600	ZNF genes & repeats	Adipose Nuclei	Adipose
27	chr19:38310800-38314000	Strong transcription	Fetal Lung	lung
28	chr19:38311000-38313800	Weak transcription	Brain Substantia Nigra	brain
29	chr19:38311000-38314400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr19:38311400-38314600	Weak transcription	Fetal Stomach	stomach
31	chr19:38312000-38313400	ZNF genes & repeats	Aorta	Aorta
32	chr19:38312000-38315000	Strong transcription	Fetal Intestine Large	intestine
33	chr19:38312000-38317400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
34	chr19:38312000-38317800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
35	chr19:38312000-38317800	ZNF genes & repeats	Ovary	ovary
36	chr19:38312000-38318400	ZNF genes & repeats	Brain Germinal Matrix	brain
37	chr19:38312000-38324000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
38	chr19:38312200-38313600	Strong transcription	Left Ventricle	heart
39	chr19:38312200-38314400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:38312400-38313200	Weak transcription	Colon Smooth Muscle	Colon
41	chr19:38312400-38313600	ZNF genes & repeats	Brain Anterior Caudate	brain
42	chr19:38312400-38313800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
43	chr19:38312400-38314400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr19:38312400-38314400	Weak transcription	Fetal Kidney	kidney
45	chr19:38312600-38315000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr19:38312800-38313200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:38312800-38314600	Weak transcription	Brain Hippocampus Middle	brain
48	chr19:38312800-38316000	ZNF genes & repeats	Liver	Liver
49	chr19:38313000-38318800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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