Variant report

Variant	rs588568
Chromosome Location	chr19:56098846-56098847
allele	C/G
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56096999..56099797-chr19:56105951..56108003,2	MCF-7	breast:
2	chr19:56098772..56100452-chr19:56100661..56102201,3	K562	blood:
3	chr19:56098772..56100429-chr19:56100677..56102201,2	K562	blood:
4	chr19:56098773..56102057-chr19:56102785..56106000,5	K562	blood:
5	chr19:56097280..56100272-chr19:56145611..56147149,2	MCF-7	breast:
6	chr19:55850192..55852001-chr19:56096983..56099024,2	MCF-7	breast:
7	chr19:56088941..56095211-chr19:56096718..56100390,8	K562	blood:
8	chr19:55918624..55921043-chr19:56097395..56100015,2	K562	blood:
9	chr19:56036876..56039163-chr19:56097331..56098917,2	MCF-7	breast:
10	chr19:56090646..56094002-chr19:56097318..56099978,3	MCF-7	breast:
11	chr19:56027946..56028668-chr19:56098469..56099189,2	MCF-7	breast:
12	chr19:56061047..56063774-chr19:56096862..56098969,2	MCF-7	breast:
13	chr19:56098521..56100588-chr19:56100809..56103773,2	MCF-7	breast:
14	chr19:56037840..56039622-chr19:56098550..56100478,2	MCF-7	breast:
15	chr19:56097571..56102985-chr19:56113573..56116936,6	K562	blood:
16	chr19:55917619..55919314-chr19:56097320..56099806,2	K562	blood:
17	chr19:56028717..56031464-chr19:56098193..56100139,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261221	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000218891	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10405287	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11084403	0.82[AFR][1000 genomes]
rs12974235	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2902746	0.82[AFR][1000 genomes]
rs2902749	1.00[YRI][hapmap]
rs310469	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs588115	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7247236	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7257888	0.82[AFR][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	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	86 gene(s)	inside rSNPs	diseases
12	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56096800-56099000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr19:56096800-56099200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr19:56096800-56099200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:56096800-56099200	Active TSS	Fetal Kidney	kidney
5	chr19:56096800-56099400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:56097000-56099000	Enhancers	Lung	lung
7	chr19:56097000-56099200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:56097000-56099200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:56097000-56099200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr19:56097000-56099200	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr19:56097000-56099200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr19:56097200-56099000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr19:56097400-56099200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr19:56097400-56099400	Enhancers	Spleen	Spleen
15	chr19:56097800-56099000	Enhancers	Fetal Lung	lung
16	chr19:56097800-56106600	Weak transcription	Aorta	Aorta
17	chr19:56098200-56099000	Flanking Active TSS	Primary B cells from peripheral blood	blood
18	chr19:56098200-56099000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:56098200-56099000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:56098200-56099000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr19:56098200-56099000	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr19:56098200-56099000	Flanking Active TSS	Fetal Thymus	thymus
23	chr19:56098200-56099000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
24	chr19:56098200-56099000	Flanking Active TSS	NHEK	skin
25	chr19:56098200-56099200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
26	chr19:56098200-56099200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr19:56098200-56099200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr19:56098200-56099200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr19:56098200-56099600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr19:56098400-56099000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr19:56098400-56099000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:56098400-56099000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:56098400-56099000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr19:56098400-56099000	Flanking Active TSS	Fetal Brain Male	brain
35	chr19:56098400-56099000	Active TSS	Stomach Mucosa	stomach
36	chr19:56098400-56099000	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr19:56098400-56099000	Active TSS	NHDF-Ad	bronchial
38	chr19:56098400-56099200	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr19:56098400-56099200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:56098400-56099200	Active TSS	Ovary	ovary
41	chr19:56098400-56099200	Flanking Active TSS	Hela-S3	cervix
42	chr19:56098400-56103400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:56098600-56099000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr19:56098600-56099000	Active TSS	Colon Smooth Muscle	Colon
45	chr19:56098600-56099000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr19:56098600-56099000	Flanking Active TSS	Right Atrium	heart
47	chr19:56098600-56099200	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr19:56098600-56099200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:56098600-56099200	Active TSS	Brain Germinal Matrix	brain
50	chr19:56098600-56099200	Active TSS	Brain Hippocampus Middle	brain

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