Variant report

Variant	rs10406552
Chromosome Location	chr19:20311515-20311516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10402115	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10402155	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10402722	1.00[AMR][1000 genomes]
rs10404469	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404767	1.00[AMR][1000 genomes]
rs10405110	1.00[AMR][1000 genomes]
rs10406926	1.00[AMR][1000 genomes]
rs10408168	1.00[AMR][1000 genomes]
rs10408369	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408777	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10410951	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412006	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412042	1.00[AMR][1000 genomes]
rs10413166	1.00[AMR][1000 genomes]
rs10414005	1.00[AMR][1000 genomes]
rs10414093	1.00[AMR][1000 genomes]
rs10414627	1.00[AMR][1000 genomes]
rs10416696	1.00[AMR][1000 genomes]
rs10417651	1.00[AMR][1000 genomes]
rs10419576	1.00[AMR][1000 genomes]
rs10420381	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420815	1.00[AMR][1000 genomes]
rs10421160	1.00[AMR][1000 genomes]
rs10421320	1.00[AMR][1000 genomes]
rs10422287	1.00[AMR][1000 genomes]
rs10424049	1.00[AMR][1000 genomes]
rs10424101	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424275	1.00[AMR][1000 genomes]
rs10427104	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13343888	1.00[AMR][1000 genomes]
rs13344384	1.00[AMR][1000 genomes]
rs13344637	0.91[AFR][1000 genomes]
rs13345082	1.00[AMR][1000 genomes]
rs2017452	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28402094	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28447348	1.00[AMR][1000 genomes]
rs28507750	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28514435	1.00[AMR][1000 genomes]
rs28526012	1.00[AMR][1000 genomes]
rs28567705	1.00[AMR][1000 genomes]
rs28690849	1.00[AMR][1000 genomes]
rs28767893	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28828686	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59440664	1.00[AMR][1000 genomes]
rs9917066	1.00[AMR][1000 genomes]
rs9967629	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking 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 miRNA	56 gene(s)	inside rSNPs	diseases
2	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
6	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers 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 miRNA	43 gene(s)	inside rSNPs	diseases
8	nsv870354	chr19:20043821-20576175	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
9	nsv1066004	chr19:20053658-20592867	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
10	nsv543932	chr19:20053658-20592867	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
11	nsv1066564	chr19:20056348-20595412	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv1066375	chr19:20061084-20574512	Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
13	nsv543934	chr19:20061084-20574512	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
14	nsv1057309	chr19:20072886-20595412	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
15	nsv578801	chr19:20084681-20595412	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
16	nsv1055694	chr19:20088866-20595412	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
17	nsv578802	chr19:20091702-20595412	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
18	nsv1064400	chr19:20101052-20595412	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
19	nsv911325	chr19:20151257-21071548	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
20	nsv1066014	chr19:20165112-20595412	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20280000-20315200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:20295400-20316800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:20298600-20312200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:20298800-20312200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:20299200-20313000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:20300200-20326400	Weak transcription	Pancreas	Pancrea
7	chr19:20305000-20314400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:20305200-20312400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:20307400-20311800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr19:20308800-20311800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr19:20308800-20315800	Weak transcription	HUVEC	blood vessel
12	chr19:20308800-20326200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:20309000-20312000	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr19:20309600-20313600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:20309600-20326200	Weak transcription	Ovary	ovary
16	chr19:20309600-20329000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:20309800-20311600	Weak transcription	NH-A	brain
18	chr19:20309800-20311800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr19:20310200-20311800	Weak transcription	HSMM	muscle
20	chr19:20310200-20314600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:20310400-20313400	Weak transcription	Fetal Brain Male	brain
22	chr19:20310400-20313800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:20310400-20315800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr19:20310400-20319200	Weak transcription	Fetal Lung	lung
25	chr19:20310400-20332400	Weak transcription	Placenta	Placenta
26	chr19:20310600-20313800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:20310600-20335800	Weak transcription	Fetal Stomach	stomach
28	chr19:20310800-20312800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:20310800-20313200	Weak transcription	Dnd41	blood
30	chr19:20310800-20313400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:20310800-20316000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:20311000-20311600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:20311000-20311800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:20311000-20311800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:20311000-20311800	Weak transcription	Fetal Intestine Small	intestine
36	chr19:20311000-20312800	Weak transcription	Brain Germinal Matrix	brain
37	chr19:20311000-20313600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:20311000-20326400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr19:20311000-20338400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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