Variant report

Variant	rs429358
Chromosome Location	chr19:45411941-45411942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:45406430..45412448-chr19:45445993..45451546,6	K562	blood:
2	chr19:45409871..45413630-chr19:45417200..45419965,4	MCF-7	breast:
3	chr19:45409844..45412639-chr19:45456918..45459928,3	K562	blood:
4	chr19:45405563..45412018-chr19:45456830..45459683,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF296-6	chr19:45411791-45412270	NONHSAT066732

Variant related genes	Relation type
ENSG00000267114	Chromatin interaction
ENSG00000130208	Chromatin interaction
ENSG00000234906	Chromatin interaction
ENSG00000104853	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10119	0.87[ASN][1000 genomes]
rs12721046	0.82[ASN][1000 genomes]
rs12721051	0.83[ASN][1000 genomes]
rs2927457	1.00[JPT][hapmap]
rs4420638	0.83[ASN][1000 genomes]
rs56131196	0.83[ASN][1000 genomes]
rs73052335	0.83[ASN][1000 genomes]
rs769449	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912129	chr19:45379791-45448465	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv912130	chr19:45382034-45448465	Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv912131	chr19:45391582-45415640	Flanking Active TSS Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv912132	chr19:45393473-45415640	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912133	chr19:45395619-45482884	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
6	nsv912134	chr19:45395619-45528799	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv912135	chr19:45408312-45415640	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv912136	chr19:45408836-45413874	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv912137	chr19:45408836-45415640	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv912138	chr19:45409113-45415640	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv912139	chr19:45410444-45415640	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:5)

Disease	PMID	Source
Alzheimer's disease biomarkers	23419831	GWAS catalog
Lewy body disease	25188341	GWAS catalog
Alzheimer's disease biomarkers	21123754	GWAS catalog
Cerebrospinal AB1-42 levels in Alzheimer's disease dementia	25027320	GWAS catalog
Brain imaging	20100581	GWAS catalog

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45400400-45414200	Weak transcription	Hela-S3	cervix
2	chr19:45406800-45414200	Weak transcription	Lung	lung
3	chr19:45409400-45414200	Weak transcription	Gastric	stomach
4	chr19:45409600-45414200	Weak transcription	HMEC	breast
5	chr19:45409600-45414400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:45410000-45413200	Weak transcription	Adipose Nuclei	Adipose
7	chr19:45410000-45413600	Weak transcription	A549	lung
8	chr19:45410000-45414200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:45410000-45414200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:45410000-45414200	Weak transcription	Fetal Lung	lung
11	chr19:45410000-45414200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:45410000-45414200	Weak transcription	HSMMtube	muscle
13	chr19:45410000-45414400	Weak transcription	Colonic Mucosa	Colon
14	chr19:45410000-45414400	Weak transcription	Esophagus	oesophagus
15	chr19:45410000-45414600	Weak transcription	Right Atrium	heart
16	chr19:45410000-45417400	Weak transcription	Fetal Heart	heart
17	chr19:45410000-45417400	Weak transcription	Pancreas	Pancrea
18	chr19:45410200-45412600	Weak transcription	Fetal Muscle Leg	muscle
19	chr19:45410200-45412800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:45410200-45413000	Weak transcription	K562	blood
21	chr19:45410200-45413200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:45410200-45414200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:45410200-45414200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:45410200-45414200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:45410200-45414600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:45410200-45417400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr19:45410400-45412000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:45410400-45412600	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr19:45410400-45412600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:45410400-45412800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:45410400-45412800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr19:45410400-45413000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:45410400-45413400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:45410400-45413400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr19:45410400-45414200	Weak transcription	Spleen	Spleen
36	chr19:45410600-45412000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:45410600-45412000	Flanking Active TSS	Liver	Liver
38	chr19:45410600-45413400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:45410800-45412000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:45410800-45412600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr19:45411000-45412600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:45411000-45412800	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr19:45411000-45412800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr19:45411000-45413400	Strong transcription	Fetal Stomach	stomach
45	chr19:45411200-45412800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:45411200-45414200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:45411400-45412000	Active TSS	Brain Anterior Caudate	brain
48	chr19:45411400-45412400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr19:45411400-45412600	Strong transcription	Ovary	ovary
50	chr19:45411400-45413000	Weak transcription	HepG2	liver

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