Variant report

Variant	rs10408589
Chromosome Location	chr19:39916971-39916972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39911800..39914936-chr19:39915871..39918478,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLEKHG2-1	chr19:39916575-39919055	ENSG00000269410.1

Variant related genes	Relation type
ENSG00000090924	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10409917	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10410092	0.86[AFR][1000 genomes]
rs10413140	1.00[EUR][1000 genomes]
rs10413673	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10415077	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10415279	1.00[EUR][1000 genomes]
rs13346052	1.00[EUR][1000 genomes]
rs2230765	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4100178	1.00[EUR][1000 genomes]
rs6508847	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
3	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
5	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
7	nsv911688	chr19:39891219-39919538	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
10	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39904800-39921000	Weak transcription	Small Intestine	intestine
2	chr19:39904800-39925800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:39905000-39921200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:39905200-39918800	Weak transcription	Pancreas	Pancrea
5	chr19:39905400-39921200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:39905400-39921200	Weak transcription	K562	blood
7	chr19:39905400-39923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:39905600-39921600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr19:39905800-39917000	Strong transcription	Thymus	Thymus
10	chr19:39905800-39918000	Weak transcription	HepG2	liver
11	chr19:39905800-39923000	Weak transcription	Brain Anterior Caudate	brain
12	chr19:39905800-39923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:39906200-39919000	Weak transcription	HMEC	breast
14	chr19:39906400-39917200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr19:39906400-39921200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr19:39907000-39917200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:39907000-39919000	Weak transcription	Right Atrium	heart
18	chr19:39907200-39917200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:39907600-39918200	Weak transcription	Fetal Heart	heart
20	chr19:39907800-39917000	Strong transcription	Fetal Stomach	stomach
21	chr19:39907800-39918200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr19:39908000-39917200	Strong transcription	Primary T cells from cord blood	blood
23	chr19:39908400-39917200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:39908600-39917000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr19:39910000-39918400	Weak transcription	Hela-S3	cervix
26	chr19:39910000-39921000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:39910000-39921200	Weak transcription	NHEK	skin
28	chr19:39910000-39922600	Weak transcription	Liver	Liver
29	chr19:39911400-39923400	Weak transcription	Fetal Brain Male	brain
30	chr19:39913000-39918400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr19:39913000-39918400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr19:39913600-39921400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr19:39913800-39922800	Weak transcription	Psoas Muscle	Psoas
34	chr19:39914000-39921000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr19:39914000-39921000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:39914200-39917400	Genic enhancers	HSMMtube	muscle
37	chr19:39914400-39918000	Weak transcription	Colonic Mucosa	Colon
38	chr19:39914800-39921600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:39915200-39918400	Weak transcription	Left Ventricle	heart
40	chr19:39915200-39918400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:39915200-39918400	Weak transcription	NHDF-Ad	bronchial
42	chr19:39915200-39918600	Weak transcription	Colon Smooth Muscle	Colon
43	chr19:39915200-39918800	Weak transcription	HUVEC	blood vessel
44	chr19:39915200-39920600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:39915200-39921600	Weak transcription	Primary B cells from cord blood	blood
46	chr19:39915200-39921600	Weak transcription	Esophagus	oesophagus
47	chr19:39915400-39918200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr19:39915400-39918400	Weak transcription	Adipose Nuclei	Adipose
49	chr19:39915400-39918400	Weak transcription	Ovary	ovary
50	chr19:39915400-39918800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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