Variant report

Variant	rs546589
Chromosome Location	chr19:37441462-37441463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1227564	0.81[AFR][1000 genomes]
rs1363751	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1363753	0.81[EUR][1000 genomes]
rs1375476	0.92[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1375477	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1612652	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1623796	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs1624087	0.92[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1625963	0.89[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1626675	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1643418	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1644634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1644637	0.89[CEU][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs1644647	0.89[CEU][hapmap];0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1644650	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1644651	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1644652	0.80[EUR][1000 genomes]
rs1644662	0.83[EUR][1000 genomes]
rs1644669	0.82[EUR][1000 genomes]
rs1644672	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1644673	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1667330	0.89[CEU][hapmap];0.85[CHB][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1667333	0.89[CEU][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1667335	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1667336	0.80[EUR][1000 genomes]
rs1667337	0.80[EUR][1000 genomes]
rs1667341	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1667351	0.85[CHB][hapmap]
rs1667353	0.89[CEU][hapmap]
rs1667354	0.81[EUR][1000 genomes]
rs1667372	0.81[AFR][1000 genomes]
rs1667378	0.85[AFR][1000 genomes]
rs1667383	0.86[AFR][1000 genomes]
rs2547054	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2551049	0.80[AFR][1000 genomes]
rs2551062	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2595545	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs4806408	0.82[YRI][hapmap]
rs496730	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs500126	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs520288	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs523979	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs524933	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs533863	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs538534	0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs541966	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs542729	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs543609	0.90[AFR][1000 genomes]
rs548077	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs560480	0.90[AFR][1000 genomes]
rs560541	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs571294	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs578977	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs580846	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7245882	0.81[YRI][hapmap]
rs7259605	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7260599	0.81[YRI][hapmap]
rs826263	0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs826295	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs826298	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs826305	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826306	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826320	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs826327	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised 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	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers 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 target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers 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 target site	73 gene(s)	inside rSNPs	diseases
6	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription 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	14 gene(s)	inside rSNPs	diseases
9	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
12	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers 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 target site	25 gene(s)	inside rSNPs	diseases
13	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
14	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
15	nsv523848	chr19:37357289-37487632	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS 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 target site	7 gene(s)	inside rSNPs	diseases
16	nsv833818	chr19:37427808-37602800	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
17	nsv579463	chr19:37437106-37488055	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
18	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS 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 target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs546589	AC012309.5	cis	Thyroid	GTEx
rs546589	ZNF585B	cis	Artery Tibial	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37409000-37444800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:37409000-37447400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:37415800-37444600	ZNF genes & repeats	Liver	Liver
4	chr19:37419400-37447400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:37420600-37443000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr19:37420600-37447400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:37420600-37447600	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr19:37427200-37441600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr19:37430800-37443200	Weak transcription	Pancreas	Pancrea
10	chr19:37433000-37442000	ZNF genes & repeats	Ovary	ovary
11	chr19:37435200-37442600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:37435400-37444400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:37436000-37441600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
14	chr19:37436000-37442000	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr19:37437400-37442600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:37437600-37441800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:37437800-37441800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
18	chr19:37437800-37441800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
19	chr19:37437800-37442000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:37437800-37442000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:37437800-37442400	ZNF genes & repeats	Brain Hippocampus Middle	brain
22	chr19:37438000-37441600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:37438000-37442000	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr19:37438200-37441600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:37438200-37441600	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:37438200-37441600	Strong transcription	Placenta	Placenta
27	chr19:37438200-37441800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr19:37438200-37441800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:37438200-37441800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
30	chr19:37438200-37442000	ZNF genes & repeats	Primary T cells from cord blood	blood
31	chr19:37438200-37442000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
32	chr19:37438200-37442000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:37438200-37442000	ZNF genes & repeats	Brain Substantia Nigra	brain
34	chr19:37438200-37442000	ZNF genes & repeats	Colon Smooth Muscle	Colon
35	chr19:37438200-37442000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
36	chr19:37438200-37442000	ZNF genes & repeats	Fetal Lung	lung
37	chr19:37438200-37442000	ZNF genes & repeats	HSMM	muscle
38	chr19:37438200-37442000	ZNF genes & repeats	NH-A	brain
39	chr19:37438200-37442000	ZNF genes & repeats	NHDF-Ad	bronchial
40	chr19:37438200-37442200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:37438200-37442200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
42	chr19:37438200-37442200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
43	chr19:37438200-37442200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
44	chr19:37438200-37442200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
45	chr19:37438200-37442200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:37438200-37442200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
47	chr19:37438200-37442400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:37438200-37442400	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
49	chr19:37438200-37442400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
50	chr19:37438200-37442400	ZNF genes & repeats	Stomach Smooth Muscle	stomach

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