Variant report

Variant	rs12973407
Chromosome Location	chr19:56928121-56928122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10408270	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10408604	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10413169	0.89[ASN][1000 genomes]
rs10415307	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10416345	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10419332	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10421407	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10432288	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11084446	0.84[EUR][1000 genomes]
rs11084449	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11084450	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11667815	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12460342	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12608966	0.84[EUR][1000 genomes]
rs12609819	0.82[EUR][1000 genomes]
rs12610115	0.88[EUR][1000 genomes]
rs12981146	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12981443	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542038	0.86[JPT][hapmap]
rs1542039	0.86[JPT][hapmap]
rs2288860	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs28373215	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2904016	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs2904017	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35027158	0.89[ASN][1000 genomes]
rs35869148	0.89[ASN][1000 genomes]
rs35914474	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745826	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3760849	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3810340	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281830	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801163	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4801319	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56301546	0.86[EUR][1000 genomes]
rs59858465	0.86[EUR][1000 genomes]
rs62121590	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62121593	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248278	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7250817	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7252607	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258010	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs728232	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8104319	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104585	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112531	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8112935	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs917650	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917651	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917652	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304776	0.89[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9749140	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9789281	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	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
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers 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 target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv544096	chr19:56905651-56933455	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12973407	ZNF582-AS1	cis	Artery Tibial	GTEx
rs12973407	ZNF582-AS1	cis	lung	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56916000-56938600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:56916400-56929800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
3	chr19:56916400-56936600	ZNF genes & repeats	Brain Germinal Matrix	brain
4	chr19:56916400-56956000	ZNF genes & repeats	Liver	Liver
5	chr19:56916600-56935600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:56916600-56956000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:56916800-56936200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:56916800-56936200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:56917000-56931000	ZNF genes & repeats	Fetal Muscle Leg	muscle
10	chr19:56917000-56931200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:56917000-56937000	ZNF genes & repeats	Fetal Lung	lung
12	chr19:56917000-56938800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:56917000-56940000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr19:56917200-56929800	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr19:56917200-56935800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:56917200-56936600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
17	chr19:56917200-56936600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr19:56917200-56937600	ZNF genes & repeats	Fetal Brain Female	brain
19	chr19:56917400-56944800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:56917600-56939400	ZNF genes & repeats	Primary T cells from cord blood	blood
21	chr19:56918200-56929800	ZNF genes & repeats	Ovary	ovary
22	chr19:56918200-56930200	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr19:56918200-56930400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:56918200-56935000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
25	chr19:56918200-56936000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr19:56918200-56937600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:56918200-56938400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:56918200-56940000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
29	chr19:56918200-56940600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
30	chr19:56918200-56943400	ZNF genes & repeats	Brain Anterior Caudate	brain
31	chr19:56918400-56928800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:56918400-56930400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
33	chr19:56918400-56931000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:56918400-56935200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
35	chr19:56918400-56935600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
36	chr19:56918400-56936600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr19:56918400-56938600	ZNF genes & repeats	Brain Hippocampus Middle	brain
38	chr19:56918400-56942800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
39	chr19:56918400-56945400	ZNF genes & repeats	Adipose Nuclei	Adipose
40	chr19:56922600-56930400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
41	chr19:56923400-56928600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
42	chr19:56924200-56930200	ZNF genes & repeats	Fetal Intestine Large	intestine
43	chr19:56925000-56929400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:56925200-56929400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
45	chr19:56925800-56928200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr19:56925800-56928600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr19:56925800-56928600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:56926000-56928200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:56926000-56929000	Weak transcription	K562	blood
50	chr19:56926000-56929200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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