Variant report

Variant	rs61741212
Chromosome Location	chr19:36157740-36157741
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11667254	0.87[ASN][1000 genomes]
rs2311871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4363955	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4805137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806189	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67400004	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv543995	chr19:36139204-36203592	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
6	nsv526166	chr19:36156588-36159368	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv817832	chr19:36156588-36159368	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
9	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs61741212	UPK1A-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs61741212	UPK1A-AS1	cis	Esophagus Mucosa	GTEx
rs61741212	UPK1A	cis	Skin Sun Exposed Lower leg	GTEx
rs61741212	UPK1A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36140400-36164000	Weak transcription	Right Atrium	heart
2	chr19:36142200-36157800	Weak transcription	Fetal Heart	heart
3	chr19:36149600-36158200	Weak transcription	Colon Smooth Muscle	Colon
4	chr19:36149600-36164000	Weak transcription	HMEC	breast
5	chr19:36149800-36158000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:36149800-36158200	Weak transcription	NH-A	brain
7	chr19:36149800-36158400	Weak transcription	Fetal Brain Male	brain
8	chr19:36149800-36158400	Weak transcription	Small Intestine	intestine
9	chr19:36149800-36161600	Weak transcription	Osteobl	bone
10	chr19:36149800-36163400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:36150000-36158000	Weak transcription	Fetal Brain Female	brain
12	chr19:36150000-36160800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:36151000-36158200	Weak transcription	Colonic Mucosa	Colon
14	chr19:36151000-36158400	Weak transcription	Fetal Intestine Large	intestine
15	chr19:36151200-36158000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:36151200-36158200	Weak transcription	NHEK	skin
17	chr19:36151200-36158400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:36151200-36158600	Weak transcription	Brain Germinal Matrix	brain
19	chr19:36151200-36158600	Weak transcription	NHLF	lung
20	chr19:36151200-36159200	Weak transcription	Ovary	ovary
21	chr19:36151200-36159200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr19:36151200-36159400	Weak transcription	A549	lung
23	chr19:36151200-36160800	Weak transcription	Brain Substantia Nigra	brain
24	chr19:36151200-36160800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:36152600-36158200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr19:36152600-36158200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:36152600-36158600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:36152600-36159800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:36152600-36160800	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:36152600-36161000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr19:36152800-36162600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr19:36153000-36164000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr19:36153400-36160000	Weak transcription	HepG2	liver
34	chr19:36153600-36159600	Weak transcription	Primary B cells from cord blood	blood
35	chr19:36155000-36159000	Weak transcription	Hela-S3	cervix
36	chr19:36155000-36159600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr19:36155200-36157800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:36155200-36158400	Weak transcription	Adipose Nuclei	Adipose
39	chr19:36155200-36158400	Weak transcription	Psoas Muscle	Psoas
40	chr19:36155200-36159800	Weak transcription	Brain Angular Gyrus	brain
41	chr19:36155400-36161000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:36155600-36164000	Weak transcription	HSMM	muscle
43	chr19:36156200-36158000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr19:36156200-36164000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:36156400-36158400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr19:36156400-36160600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:36156600-36159000	Weak transcription	Aorta	Aorta
48	chr19:36156600-36159200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:36156600-36159200	Weak transcription	Liver	Liver
50	chr19:36156600-36160600	Weak transcription	Brain Inferior Temporal Lobe	brain

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