Variant report

Variant	rs1862645
Chromosome Location	chr19:18724316-18724317
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18722600-18724393	H1-neurons	neurons:	n/a	n/a
2	SUZ12	chr19:18722639-18725317	NT2-D1	testis:	n/a	n/a
3	MAZ	chr19:18722480-18724396	IMR90	lung:	n/a	chr19:18722557-18722566 chr19:18722554-18722564 chr19:18722553-18722561 chr19:18722555-18722564 chr19:18722555-18722564 chr19:18722555-18722564
4	ZNF263	chr19:18724174-18724490	HEK293-T-REx	kidney:	n/a	chr19:18724418-18724427 chr19:18724259-18724268 chr19:18724245-18724266 chr19:18724379-18724388
5	REST	chr19:18722789-18724545	H1-neurons	neurons:	n/a	chr19:18723951-18723964 chr19:18722993-18723006 chr19:18723682-18723692

No.	Distal block	Cell Line	Cell type
1	chr19:18708097..18710624-chr19:18723730..18725738,2	K562	blood:
2	chr19:18714829..18718349-chr19:18723409..18727026,4	K562	blood:
3	chr19:18715795..18719274-chr19:18719391..18724999,7	MCF-7	breast:
4	chr19:18713204..18718867-chr19:18719015..18725496,7	MCF-7	breast:

Variant related genes	Relation type
TMEM59L	TF binding region
ENSG00000105696	Chromatin interaction
ENSG00000006016	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10409392	0.81[JPT][hapmap]
rs1043192	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12609505	0.81[JPT][hapmap]
rs1468475	0.81[JPT][hapmap]
rs2057649	0.90[JPT][hapmap]
rs2074175	0.90[JPT][hapmap]
rs2079015	0.90[JPT][hapmap]
rs2238650	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2283616	0.82[JPT][hapmap]
rs2302055	0.81[JPT][hapmap]
rs2314664	0.90[JPT][hapmap]
rs2314665	0.90[JPT][hapmap]
rs2314666	0.86[JPT][hapmap]
rs3170474	0.95[JPT][hapmap]
rs3761032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4808137	0.81[JPT][hapmap]
rs4808138	0.90[ASN][1000 genomes]
rs4808823	0.90[JPT][hapmap]
rs4808839	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6554	0.81[JPT][hapmap]
rs709679	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7250192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7250623	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs7256319	0.95[JPT][hapmap]
rs7259557	0.91[ASN][1000 genomes]
rs7648	0.82[JPT][hapmap]
rs916791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer 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	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911287	chr19:18699333-18727913	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv911288	chr19:18700047-18739497	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv911291	chr19:18701499-18726856	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
12	nsv911292	chr19:18701499-18731658	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18721200-18724400	Bivalent Enhancer	Placenta	Placenta
2	chr19:18721600-18724400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:18721600-18724600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:18721600-18724600	Bivalent Enhancer	Fetal Heart	heart
5	chr19:18721800-18724600	Bivalent Enhancer	Fetal Lung	lung
6	chr19:18721800-18725000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:18722400-18724600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr19:18722400-18724800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr19:18722400-18725200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:18722600-18724400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
11	chr19:18723400-18724400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:18723400-18724400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
13	chr19:18723400-18724600	Active TSS	Brain Substantia Nigra	brain
14	chr19:18723400-18724800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr19:18723400-18725000	Active TSS	Brain Anterior Caudate	brain
16	chr19:18723400-18725200	Active TSS	Brain Angular Gyrus	brain
17	chr19:18723400-18725200	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr19:18723600-18724400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:18723600-18724400	Bivalent Enhancer	Fetal Intestine Large	intestine
20	chr19:18723600-18724600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr19:18723600-18725000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr19:18723800-18724400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:18723800-18724400	Bivalent Enhancer	Spleen	Spleen
24	chr19:18724000-18724400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:18724000-18724400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:18724000-18724400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:18724000-18724400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr19:18724000-18724400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
29	chr19:18724000-18724400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:18724000-18724400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
31	chr19:18724000-18724400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:18724000-18724400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:18724000-18724400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:18724000-18724400	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr19:18724000-18724400	Bivalent Enhancer	Colonic Mucosa	Colon
36	chr19:18724000-18724400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
37	chr19:18724000-18724400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr19:18724000-18724400	Flanking Bivalent TSS/Enh	HepG2	liver
39	chr19:18724000-18724600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
40	chr19:18724000-18724800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:18724000-18724800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
42	chr19:18724000-18725600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:18724200-18724400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
44	chr19:18724200-18724400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
45	chr19:18724200-18724400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:18724200-18724400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:18724200-18724400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
48	chr19:18724200-18724400	Flanking Active TSS	Fetal Brain Male	brain
49	chr19:18724200-18724400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
50	chr19:18724200-18724400	Bivalent Enhancer	Fetal Kidney	kidney

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