Variant report

Variant	rs10412409
Chromosome Location	chr19:19914513-19914514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10407920	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10419635	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10854013	0.91[ASN][1000 genomes]
rs11878280	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12461018	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12973032	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12975121	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2304171	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2335360	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs23654	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248955	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2878398	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34277739	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35018071	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35280091	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4990741	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60041535	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7246983	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252985	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8104136	0.80[ASN][1000 genomes]
rs8108416	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919785	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription 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 target site	67 gene(s)	inside rSNPs	diseases
2	nsv911312	chr19:19861682-19917662	Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription 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	15 gene(s)	inside rSNPs	diseases
6	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription 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	27 gene(s)	inside rSNPs	diseases
7	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
8	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases
10	nsv578799	chr19:19901136-19967970	ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10412409	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19888400-19927800	Weak transcription	Psoas Muscle	Psoas
2	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
3	chr19:19895000-19931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:19895400-19914800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:19895400-19914800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:19895600-19914800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:19895600-19915000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
8	chr19:19895800-19914800	Strong transcription	Dnd41	blood
9	chr19:19897200-19918600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:19900000-19915200	Weak transcription	HepG2	liver
11	chr19:19902600-19922400	Weak transcription	Right Ventricle	heart
12	chr19:19902600-19931600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:19903200-19916400	Weak transcription	Fetal Brain Male	brain
14	chr19:19905000-19930000	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:19906400-19920400	Weak transcription	Brain Angular Gyrus	brain
16	chr19:19906400-19923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:19906800-19916200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr19:19907000-19916200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr19:19907000-19916400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:19907000-19923200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:19907000-19931400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr19:19907000-19931600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr19:19907200-19915800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:19907600-19929600	Weak transcription	Small Intestine	intestine
25	chr19:19907800-19931600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:19908000-19931600	Weak transcription	Stomach Mucosa	stomach
27	chr19:19909000-19914800	Strong transcription	Fetal Lung	lung
28	chr19:19909200-19931600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:19909800-19914800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr19:19909800-19914800	ZNF genes & repeats	Liver	Liver
31	chr19:19909800-19915000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
32	chr19:19910000-19914600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:19910200-19914800	ZNF genes & repeats	Primary T cells from cord blood	blood
34	chr19:19910400-19914600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:19910400-19914600	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr19:19910400-19914800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr19:19910600-19915000	ZNF genes & repeats	Primary B cells from cord blood	blood
38	chr19:19911200-19914600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:19911400-19914600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
40	chr19:19911400-19914600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr19:19911400-19914600	Strong transcription	Fetal Muscle Leg	muscle
42	chr19:19911600-19914600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr19:19911600-19914800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:19911600-19915000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
45	chr19:19911800-19915000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:19912400-19921600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:19912600-19914800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
48	chr19:19913000-19916400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr19:19913400-19914600	Strong transcription	Fetal Thymus	thymus
50	chr19:19913400-19914800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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