Variant report

Variant	rs67400004
Chromosome Location	chr19:36159647-36159648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36153170..36155619-chr19:36159391..36161425,2	MCF-7	breast:
2	chr19:36159215..36161380-chr19:36163087..36164675,2	K562	blood:

Variant related genes	Relation type
ENSG00000266455	Chromatin interaction
ENSG00000226510	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11667254	0.87[ASN][1000 genomes]
rs2311871	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4363955	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4805137	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806189	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61741212	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
7	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
rs67400004	UPK1A	cis	Esophagus Mucosa	GTEx
rs67400004	UPK1A-AS1	cis	Esophagus Mucosa	GTEx
rs67400004	UPK1A	cis	Skin Sun Exposed Lower leg	GTEx
rs67400004	UPK1A-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36140400-36164000	Weak transcription	Right Atrium	heart
2	chr19:36149600-36164000	Weak transcription	HMEC	breast
3	chr19:36149800-36161600	Weak transcription	Osteobl	bone
4	chr19:36149800-36163400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr19:36150000-36160800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:36151200-36160800	Weak transcription	Brain Substantia Nigra	brain
7	chr19:36151200-36160800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr19:36152600-36159800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:36152600-36160800	Weak transcription	Brain Hippocampus Middle	brain
10	chr19:36152600-36161000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr19:36152800-36162600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:36153000-36164000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:36153400-36160000	Weak transcription	HepG2	liver
14	chr19:36155200-36159800	Weak transcription	Brain Angular Gyrus	brain
15	chr19:36155400-36161000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:36155600-36164000	Weak transcription	HSMM	muscle
17	chr19:36156200-36164000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:36156400-36160600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:36156600-36160600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:36156600-36164200	Weak transcription	Gastric	stomach
21	chr19:36156800-36160000	Weak transcription	Left Ventricle	heart
22	chr19:36156800-36160600	Weak transcription	Fetal Intestine Small	intestine
23	chr19:36156800-36161000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr19:36156800-36164000	Weak transcription	Spleen	Spleen
25	chr19:36157200-36160400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:36157200-36164000	Weak transcription	Esophagus	oesophagus
27	chr19:36157400-36164200	Weak transcription	Right Ventricle	heart
28	chr19:36157600-36161800	Weak transcription	Thymus	Thymus
29	chr19:36157800-36164000	Weak transcription	Pancreas	Pancrea
30	chr19:36159600-36159800	Enhancers	Fetal Thymus	thymus
31	chr19:36159600-36164000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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