Variant report

Variant	rs546082
Chromosome Location	chr19:56608425-56608426
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56607823..56609987-chr19:56630253..56632648,2	MCF-7	breast:
2	chr19:56603039..56605277-chr19:56607170..56609426,2	MCF-7	breast:
3	chr19:56601536..56604040-chr19:56606734..56609466,2	MCF-7	breast:
4	chr19:56606614..56610711-chr19:56622862..56625649,3	MCF-7	breast:
5	chr19:56589626..56592403-chr19:56608296..56610728,2	MCF-7	breast:
6	chr19:56607132..56609699-chr19:56615697..56617410,2	K562	blood:
7	chr19:56606956..56610411-chr19:56610787..56614898,5	K562	blood:

Variant related genes	Relation type
ENSG00000223060	Chromatin interaction
ENSG00000142409	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10409172	1.00[JPT][hapmap]
rs11673628	0.89[CEU][hapmap]
rs12983086	1.00[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs28553904	1.00[JPT][hapmap]
rs473045	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801676	0.80[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap]
rs490015	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs496526	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs499083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs506986	1.00[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs511610	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs511642	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs529291	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587252	0.83[EUR][1000 genomes]
rs629836	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs8103672	0.87[GIH][hapmap];1.00[TSI][hapmap]
rs9676765	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1058988	chr19:56382492-56609032	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
5	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
6	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
7	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
10	nsv912512	chr19:56592286-56636759	Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	nsv912514	chr19:56596815-56636759	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
15	nsv912515	chr19:56598829-56623710	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
16	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
17	esv1809307	chr19:56604027-56633623	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56592600-56620000	Weak transcription	HSMMtube	muscle
2	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:56593000-56616200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:56593000-56616600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:56593000-56616800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:56593600-56616000	Weak transcription	Stomach Mucosa	stomach
8	chr19:56594800-56616800	Weak transcription	HUVEC	blood vessel
9	chr19:56596600-56614800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:56597200-56619400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:56599800-56615200	Strong transcription	Liver	Liver
12	chr19:56600000-56619000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:56600400-56614400	Strong transcription	HepG2	liver
14	chr19:56600600-56609000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:56600800-56616800	Weak transcription	Small Intestine	intestine
16	chr19:56601400-56612000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:56601600-56611800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr19:56602600-56610200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr19:56602800-56614400	ZNF genes & repeats	Fetal Stomach	stomach
20	chr19:56602800-56620000	Weak transcription	NH-A	brain
21	chr19:56603000-56608800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr19:56603000-56616600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:56603200-56609000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:56603200-56612400	Weak transcription	Osteobl	bone
25	chr19:56603200-56619800	Weak transcription	NHDF-Ad	bronchial
26	chr19:56603400-56609000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:56603800-56608800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:56603800-56609000	Weak transcription	Brain Anterior Caudate	brain
29	chr19:56603800-56612200	Weak transcription	Brain Substantia Nigra	brain
30	chr19:56603800-56616800	Weak transcription	Psoas Muscle	Psoas
31	chr19:56604000-56614800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr19:56604200-56608600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:56604200-56609200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr19:56604200-56611600	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:56604800-56616200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:56604800-56616800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:56605000-56608600	Weak transcription	Hela-S3	cervix
38	chr19:56605000-56610000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:56605000-56612200	Weak transcription	Aorta	Aorta
40	chr19:56605000-56612600	Weak transcription	HMEC	breast
41	chr19:56605000-56614400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr19:56605000-56615000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:56605000-56616400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:56605200-56608600	Weak transcription	Primary T cells from cord blood	blood
45	chr19:56605200-56608600	Weak transcription	Fetal Thymus	thymus
46	chr19:56605200-56608800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:56605200-56609000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:56605200-56610200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:56605200-56610800	Weak transcription	Primary B cells from cord blood	blood
50	chr19:56605200-56615000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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