Variant report

Variant	rs17770717
Chromosome Location	chr19:53442337-53442338
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53399445..53402130-chr19:53440139..53442366,2	K562	blood:
2	chr19:53438104..53442400-chr19:53444179..53446884,10	K562	blood:

Variant related genes	Relation type
ENSG00000180257	Chromatin interaction
ENSG00000182986	Chromatin interaction
ENSG00000213801	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10402901	1.00[JPT][hapmap];0.84[MEX][hapmap]
rs55895749	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58988965	0.81[EUR][1000 genomes]
rs8110394	1.00[JPT][hapmap]

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	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
2	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
3	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
4	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
5	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
6	nsv912321	chr19:53186836-53451291	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1058903	chr19:53193570-53489633	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv1067280	chr19:53193570-53567287	Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv544062	chr19:53193570-53567287	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv580030	chr19:53194344-53547394	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1057118	chr19:53195426-53480449	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	43 gene(s)	inside rSNPs	diseases
13	nsv912323	chr19:53249347-53451291	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases
14	esv3431689	chr19:53291230-53483998	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
15	nsv912330	chr19:53317001-53478109	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
16	nsv1064234	chr19:53346827-53480449	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	esv3319159	chr19:53361167-53446431	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
18	esv3319160	chr19:53361308-53446343	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
19	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
20	nsv963071	chr19:53401720-53480869	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
22	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers 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	30 gene(s)	inside rSNPs	diseases
23	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17770717	TRIM28	cis	parietal	SCAN
rs17770717	ZNF581	cis	cerebellum	SCAN
rs17770717	ZNF471	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53426600-53444800	Weak transcription	Fetal Heart	heart
2	chr19:53426800-53444800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:53426800-53445000	Weak transcription	Small Intestine	intestine
4	chr19:53426800-53445200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:53426800-53445200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:53427000-53442600	Weak transcription	Ovary	ovary
7	chr19:53427000-53444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:53427400-53444800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:53427400-53445000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:53427400-53445200	Weak transcription	Left Ventricle	heart
11	chr19:53427600-53444600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:53427600-53444800	Weak transcription	NHDF-Ad	bronchial
13	chr19:53427800-53444800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr19:53427800-53445200	Weak transcription	NHLF	lung
15	chr19:53428600-53444800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:53432000-53444600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:53432000-53444800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:53432400-53444800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:53432400-53444800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:53432600-53442600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr19:53432600-53444800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr19:53432600-53444800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:53432600-53445000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr19:53432600-53445000	Weak transcription	Fetal Muscle Leg	muscle
25	chr19:53432600-53445000	Weak transcription	HSMMtube	muscle
26	chr19:53433000-53444600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:53433600-53444800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:53434000-53442800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:53438200-53443200	Enhancers	Stomach Mucosa	stomach
30	chr19:53438400-53444600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:53438400-53444800	Weak transcription	Right Ventricle	heart
32	chr19:53438800-53444600	Enhancers	Placenta	Placenta
33	chr19:53439000-53444800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:53439000-53444800	Weak transcription	Fetal Thymus	thymus
35	chr19:53439200-53442800	Enhancers	Fetal Intestine Large	intestine
36	chr19:53439200-53444200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:53439800-53444800	Weak transcription	Osteobl	bone
38	chr19:53440400-53444200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:53440400-53444800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:53440400-53444800	Weak transcription	Fetal Lung	lung
41	chr19:53440400-53445000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:53440600-53444600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr19:53440600-53444800	Weak transcription	Primary T cells from cord blood	blood
44	chr19:53440800-53443400	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr19:53440800-53444400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:53440800-53444400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr19:53440800-53444400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr19:53440800-53444600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr19:53440800-53444800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:53440800-53444800	Weak transcription	Primary B cells from cord blood	blood

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