Variant report

Variant	rs2285424
Chromosome Location	chr19:36499173-36499174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36497746..36499339-chr19:36508373..36509944,2	MCF-7	breast:
2	chr19:36494473..36501836-chr19:36501930..36505739,14	K562	blood:
3	chr19:36485859..36488292-chr19:36497907..36499980,3	K562	blood:
4	chr19:36496294..36501686-chr19:36543356..36547257,9	MCF-7	breast:
5	chr19:36497884..36507784-chr19:36542079..36547610,17	MCF-7	breast:
6	chr19:36499093..36500043-chr20:47894726..47895550,2	HCT-116	colon:
7	chr19:36388094..36390635-chr19:36498099..36499853,2	K562	blood:
8	chr19:36498267..36501775-chr19:36606279..36609989,4	MCF-7	breast:
9	chr19:36485859..36488292-chr19:36497907..36499980,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C19orf46-1	chr19:36499119-36499512	NONHSAT065945

No data

Variant related genes	Relation type
ENSG00000267698	Chromatin interaction
ENSG00000177410	Chromatin interaction
ENSG00000209042	Chromatin interaction
ENSG00000161277	Chromatin interaction
ENSG00000124201	Chromatin interaction
ENSG00000239382	Chromatin interaction
ENSG00000205138	Chromatin interaction
ENSG00000075702	Chromatin interaction
ENSG00000167604	Chromatin interaction
ENSG00000105254	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10403729	0.89[EUR][1000 genomes]
rs1043822	0.98[ASN][1000 genomes]
rs10469279	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12460721	0.80[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12462677	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17720402	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2073893	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2285423	0.90[ASN][1000 genomes]
rs4458134	0.90[ASN][1000 genomes]
rs4806245	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4806247	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7256169	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7258897	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv911641	chr19:36473677-36536938	Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv1000212	chr19:36494643-36508508	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2285424	ZNF235	cis	parietal	SCAN
rs2285424	PSG1	cis	cerebellum	SCAN
rs2285424	PPP1R14A	cis	parietal	SCAN
rs2285424	PLEKHG2	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36487200-36499200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:36487200-36504200	Weak transcription	HSMMtube	muscle
3	chr19:36487600-36499200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:36487600-36499800	Weak transcription	HUVEC	blood vessel
5	chr19:36487600-36500000	Weak transcription	HSMM	muscle
6	chr19:36487800-36499200	Weak transcription	HMEC	breast
7	chr19:36487800-36499600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:36487800-36499600	Weak transcription	NHEK	skin
9	chr19:36488000-36499600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:36488000-36504000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:36488400-36499400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:36488400-36499600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr19:36488400-36504200	Weak transcription	Primary B cells from cord blood	blood
14	chr19:36488600-36499600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr19:36488600-36503800	Weak transcription	GM12878-XiMat	blood
16	chr19:36488800-36499600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:36488800-36504000	Weak transcription	Hela-S3	cervix
18	chr19:36489000-36500000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:36489600-36499600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:36490200-36499400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:36490400-36499200	Weak transcription	Fetal Brain Female	brain
22	chr19:36490400-36499600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr19:36490400-36499600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr19:36490400-36499600	Weak transcription	Right Ventricle	heart
25	chr19:36490400-36499800	Weak transcription	NHDF-Ad	bronchial
26	chr19:36490600-36499800	Weak transcription	Right Atrium	heart
27	chr19:36490800-36499600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:36490800-36499800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:36490800-36500000	Weak transcription	Ovary	ovary
30	chr19:36491000-36499600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr19:36491000-36499800	Weak transcription	Colon Smooth Muscle	Colon
32	chr19:36491000-36500400	Weak transcription	NHLF	lung
33	chr19:36491200-36499400	Weak transcription	Brain Hippocampus Middle	brain
34	chr19:36491200-36499400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:36491200-36499400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:36491200-36499400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr19:36491200-36499600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:36491200-36499600	Weak transcription	Brain Substantia Nigra	brain
39	chr19:36491200-36499800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:36491200-36499800	Weak transcription	Brain Angular Gyrus	brain
41	chr19:36491200-36499800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr19:36492400-36499400	Weak transcription	A549	lung
43	chr19:36492400-36499600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr19:36492600-36499400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:36492600-36499600	Weak transcription	Primary T cells from cord blood	blood
46	chr19:36492600-36499800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr19:36492600-36500000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:36492600-36503600	Weak transcription	Dnd41	blood
49	chr19:36492600-36503800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:36492800-36499200	Weak transcription	Spleen	Spleen

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