Variant report

Variant	rs2054446
Chromosome Location	chr19:53174436-53174437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53169045..53171439-chr19:53172531..53174974,2	K562	blood:
2	chr19:53170186..53171994-chr19:53174375..53177795,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11669409	0.83[ASN][1000 genomes]
rs1975941	0.83[ASN][1000 genomes]
rs2100945	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2869084	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2904001	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6509664	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6509665	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8107738	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv912311	chr19:53103875-53212361	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv912312	chr19:53103875-53296371	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
14	nsv912318	chr19:53118278-53451291	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
15	nsv458744	chr19:53120559-53236331	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
16	nsv580028	chr19:53120559-53236331	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	esv3489404	chr19:53121944-53391394	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
18	esv3489405	chr19:53121944-53391394	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
19	nsv961238	chr19:53144650-53221094	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
20	nsv432072	chr19:53144788-53554388	Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
21	esv3401212	chr19:53151131-53482063	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
22	nsv912319	chr19:53152923-53241107	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
23	nsv912320	chr19:53164172-53243026	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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 target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2054446	AURKC	cis	parietal	SCAN
rs2054446	CNOT3	cis	parietal	SCAN
rs2054446	NDUFA3	cis	parietal	SCAN
rs2054446	ZNF304	cis	cerebellum	SCAN
rs2054446	VN1R1	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53153600-53184200	Weak transcription	Colonic Mucosa	Colon
2	chr19:53155000-53191400	Weak transcription	Colon Smooth Muscle	Colon
3	chr19:53157000-53176600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:53157200-53191600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr19:53158600-53177200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:53162600-53182600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr19:53162800-53174600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:53162800-53186600	Weak transcription	Aorta	Aorta
9	chr19:53163000-53182600	Weak transcription	Hela-S3	cervix
10	chr19:53163000-53192400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:53163200-53183000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr19:53163800-53177200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:53163800-53183200	Weak transcription	HUVEC	blood vessel
14	chr19:53163800-53188400	Weak transcription	Ovary	ovary
15	chr19:53164000-53178600	Weak transcription	Brain Germinal Matrix	brain
16	chr19:53164000-53183000	Weak transcription	Adipose Nuclei	Adipose
17	chr19:53164000-53185600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr19:53164000-53192400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:53164000-53192400	Weak transcription	NH-A	brain
20	chr19:53164000-53193000	Weak transcription	Right Ventricle	heart
21	chr19:53164200-53177200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr19:53164200-53177200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr19:53164200-53192400	Weak transcription	Brain Angular Gyrus	brain
24	chr19:53164400-53176400	Weak transcription	Fetal Lung	lung
25	chr19:53164400-53192400	Weak transcription	HSMM	muscle
26	chr19:53164600-53189200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:53164600-53192200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr19:53164800-53186400	Weak transcription	Osteobl	bone
29	chr19:53165000-53177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:53165000-53179000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr19:53165000-53191600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:53165000-53191800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr19:53165000-53192400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:53165200-53177200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:53165200-53186400	Weak transcription	Fetal Thymus	thymus
36	chr19:53165200-53186400	Weak transcription	NHLF	lung
37	chr19:53165400-53183000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:53165600-53179000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:53165600-53191800	Weak transcription	NHDF-Ad	bronchial
40	chr19:53165800-53179000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr19:53165800-53186400	Weak transcription	Pancreas	Pancrea
42	chr19:53165800-53191600	Weak transcription	Fetal Brain Female	brain
43	chr19:53166200-53182400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr19:53166400-53176400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr19:53166400-53177400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:53166400-53178600	Weak transcription	Left Ventricle	heart
47	chr19:53167800-53174800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:53168000-53176200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:53168600-53174800	Weak transcription	Spleen	Spleen
50	chr19:53168600-53175400	Weak transcription	Fetal Stomach	stomach

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