Variant report

Variant	rs10405987
Chromosome Location	chr19:52624369-52624370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10405763	0.87[ASN][1000 genomes]
rs10415918	0.90[ASN][1000 genomes]
rs10423034	0.91[ASN][1000 genomes]
rs11084145	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12162225	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12462872	0.98[ASN][1000 genomes]
rs12462908	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609137	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610551	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16983496	0.91[ASN][1000 genomes]
rs17779542	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17835808	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45468391	0.90[ASN][1000 genomes]
rs59541557	0.81[ASN][1000 genomes]
rs67861844	0.81[ASN][1000 genomes]
rs8100114	0.90[ASN][1000 genomes]
rs8105609	0.92[ASN][1000 genomes]
rs8108125	0.91[ASN][1000 genomes]
rs8112502	0.92[ASN][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	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv34938	chr19:52227916-52630935	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1060519	chr19:52270087-52628611	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv534202	chr19:52272356-52627403	Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv1059924	chr19:52273257-52628611	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv2535	chr19:52580906-52625889	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3433050	chr19:52595705-52639973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52606800-52640200	ZNF genes & repeats	Liver	Liver
2	chr19:52607000-52634000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:52609800-52639000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:52609800-52640200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:52610600-52631800	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:52612600-52629600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:52613400-52629800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
8	chr19:52613600-52629400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
9	chr19:52613600-52639000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:52615200-52640200	ZNF genes & repeats	Fetal Brain Female	brain
11	chr19:52615400-52625000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr19:52615600-52640200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:52615800-52625000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:52615800-52631400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
15	chr19:52616000-52625000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:52616200-52625000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:52616200-52631600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr19:52616200-52632600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr19:52616200-52634200	ZNF genes & repeats	Primary T cells from cord blood	blood
20	chr19:52616200-52640000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:52616200-52641200	ZNF genes & repeats	Dnd41	blood
22	chr19:52616200-52641400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:52616200-52641600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:52616400-52624800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:52616400-52625000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:52616400-52629600	ZNF genes & repeats	Primary B cells from cord blood	blood
27	chr19:52616400-52633000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr19:52616400-52641400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:52616600-52625000	ZNF genes & repeats	Brain Anterior Caudate	brain
30	chr19:52616800-52629400	ZNF genes & repeats	Fetal Lung	lung
31	chr19:52616800-52634000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
32	chr19:52617000-52640200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr19:52617200-52629600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
34	chr19:52617200-52629800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
35	chr19:52617200-52634000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
36	chr19:52617200-52640200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:52617400-52625200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:52617400-52625200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
39	chr19:52617400-52630000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
40	chr19:52617400-52632000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
41	chr19:52617400-52632400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
42	chr19:52617400-52634200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:52617400-52641400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr19:52617600-52625000	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
45	chr19:52617600-52625000	ZNF genes & repeats	Brain Hippocampus Middle	brain
46	chr19:52617600-52625000	ZNF genes & repeats	Colon Smooth Muscle	Colon
47	chr19:52617600-52625200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
48	chr19:52617600-52625600	ZNF genes & repeats	Fetal Kidney	kidney
49	chr19:52617600-52629600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:52617800-52624600	ZNF genes & repeats	Fetal Muscle Leg	muscle

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