Variant report

Variant	rs543609
Chromosome Location	chr19:37430721-37430722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37428613..37430520-chr19:37430554..37432406,2	MCF-7	breast:
2	chr19:37411760..37413673-chr19:37428843..37431824,2	MCF-7	breast:

Extended variants
information (count: 149 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1016216	0.84[EUR][1000 genomes]
rs10421398	0.83[EUR][1000 genomes]
rs10421415	0.83[EUR][1000 genomes]
rs1227564	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1345748	0.83[EUR][1000 genomes]
rs1363751	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1363752	0.83[EUR][1000 genomes]
rs1363753	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1375476	0.86[EUR][1000 genomes]
rs1375477	0.86[EUR][1000 genomes]
rs1449200	0.84[EUR][1000 genomes]
rs1449201	0.84[EUR][1000 genomes]
rs1579314	0.83[EUR][1000 genomes]
rs1612652	0.84[EUR][1000 genomes]
rs1621329	0.84[EUR][1000 genomes]
rs1623796	0.83[EUR][1000 genomes]
rs1624087	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1625963	0.86[EUR][1000 genomes]
rs1626675	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1643418	0.91[EUR][1000 genomes]
rs1644637	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1644647	0.91[EUR][1000 genomes]
rs1644648	0.83[EUR][1000 genomes]
rs1644650	0.91[EUR][1000 genomes]
rs1644651	0.91[EUR][1000 genomes]
rs1644652	0.86[EUR][1000 genomes]
rs1644654	0.85[EUR][1000 genomes]
rs1644656	0.85[EUR][1000 genomes]
rs1644657	0.84[EUR][1000 genomes]
rs1644658	0.84[EUR][1000 genomes]
rs1644659	0.84[EUR][1000 genomes]
rs1644661	0.84[EUR][1000 genomes]
rs1644662	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1644663	0.84[EUR][1000 genomes]
rs1644665	0.84[EUR][1000 genomes]
rs1644666	0.84[EUR][1000 genomes]
rs1644667	0.84[EUR][1000 genomes]
rs1644668	0.84[EUR][1000 genomes]
rs1644669	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1644670	0.84[EUR][1000 genomes]
rs1644671	0.83[EUR][1000 genomes]
rs1644672	0.83[EUR][1000 genomes]
rs1644674	0.84[EUR][1000 genomes]
rs1644675	0.84[EUR][1000 genomes]
rs1644676	0.84[EUR][1000 genomes]
rs1644677	0.84[EUR][1000 genomes]
rs1644678	0.84[EUR][1000 genomes]
rs1644679	0.83[EUR][1000 genomes]
rs1644682	0.83[EUR][1000 genomes]
rs1644683	0.83[EUR][1000 genomes]
rs1644684	0.83[EUR][1000 genomes]
rs1644685	0.83[EUR][1000 genomes]
rs1644686	0.83[EUR][1000 genomes]
rs1644687	0.83[EUR][1000 genomes]
rs1644688	0.83[EUR][1000 genomes]
rs1644689	0.83[EUR][1000 genomes]
rs1644690	0.83[EUR][1000 genomes]
rs1644693	0.83[EUR][1000 genomes]
rs1644695	0.83[EUR][1000 genomes]
rs1644698	0.83[EUR][1000 genomes]
rs1667330	0.91[EUR][1000 genomes]
rs1667333	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1667335	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1667336	0.86[EUR][1000 genomes]
rs1667337	0.86[EUR][1000 genomes]
rs1667341	0.90[EUR][1000 genomes]
rs1667342	0.85[EUR][1000 genomes]
rs1667344	0.85[EUR][1000 genomes]
rs1667346	0.83[EUR][1000 genomes]
rs1667347	0.84[EUR][1000 genomes]
rs1667348	0.84[EUR][1000 genomes]
rs1667349	0.84[EUR][1000 genomes]
rs1667350	0.84[EUR][1000 genomes]
rs1667352	0.83[EUR][1000 genomes]
rs1667353	0.84[EUR][1000 genomes]
rs1667354	0.88[EUR][1000 genomes]
rs1667355	0.83[EUR][1000 genomes]
rs1667356	0.83[EUR][1000 genomes]
rs1667358	0.83[EUR][1000 genomes]
rs1667360	0.83[EUR][1000 genomes]
rs1667363	0.83[EUR][1000 genomes]
rs1667364	0.82[EUR][1000 genomes]
rs1667366	0.83[EUR][1000 genomes]
rs1667367	0.82[EUR][1000 genomes]
rs1667378	0.83[AFR][1000 genomes]
rs1667382	0.94[EUR][1000 genomes]
rs1667383	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2432651	0.81[EUR][1000 genomes]
rs2547044	0.83[EUR][1000 genomes]
rs2547045	0.83[EUR][1000 genomes]
rs2547049	0.83[EUR][1000 genomes]
rs2547050	0.82[EUR][1000 genomes]
rs2547051	0.83[EUR][1000 genomes]
rs2547052	0.83[EUR][1000 genomes]
rs2547054	0.91[EUR][1000 genomes]
rs2551053	0.83[EUR][1000 genomes]
rs2551054	0.83[EUR][1000 genomes]
rs2551060	0.82[EUR][1000 genomes]
rs2551062	0.91[EUR][1000 genomes]
rs2595545	0.83[EUR][1000 genomes]
rs2595546	0.83[EUR][1000 genomes]
rs2595547	0.83[EUR][1000 genomes]
rs496730	0.92[EUR][1000 genomes]
rs497130	0.88[EUR][1000 genomes]
rs5008750	0.84[EUR][1000 genomes]
rs5008751	0.84[EUR][1000 genomes]
rs520288	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs523979	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs524933	0.92[EUR][1000 genomes]
rs533863	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs538534	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs538649	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs540472	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs541966	0.91[EUR][1000 genomes]
rs542729	0.91[EUR][1000 genomes]
rs543212	0.95[EUR][1000 genomes]
rs544964	0.89[ASN][1000 genomes]
rs546589	0.90[AFR][1000 genomes]
rs548077	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs560480	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs571294	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs578977	0.91[EUR][1000 genomes]
rs580846	1.00[EUR][1000 genomes]
rs7253220	0.80[EUR][1000 genomes]
rs7259605	0.91[EUR][1000 genomes]
rs826263	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826285	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs826295	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs826298	0.95[EUR][1000 genomes]
rs826320	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs860392	0.95[EUR][1000 genomes]
rs935706	0.83[EUR][1000 genomes]
rs935707	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs543609	ZNF585B	cis	Artery Tibial	GTEx
rs543609	AC012309.5	cis	Thyroid	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37408200-37436400	Weak transcription	Fetal Thymus	thymus
2	chr19:37408200-37440600	Weak transcription	Stomach Mucosa	stomach
3	chr19:37408400-37440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:37408600-37439600	Weak transcription	Fetal Heart	heart
5	chr19:37409000-37444800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:37409000-37447400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:37415800-37444600	ZNF genes & repeats	Liver	Liver
8	chr19:37419400-37447400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr19:37420600-37443000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr19:37420600-37447400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr19:37420600-37447600	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr19:37426000-37432000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:37426800-37438200	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr19:37427000-37432200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:37427200-37433800	Strong transcription	Dnd41	blood
16	chr19:37427200-37437200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:37427200-37441600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
18	chr19:37427400-37431200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:37427400-37431400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:37427400-37432400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
21	chr19:37427400-37432400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
22	chr19:37427400-37432600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr19:37427400-37432800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:37427400-37432800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr19:37427400-37437200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
26	chr19:37427400-37437400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:37427600-37431000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:37427600-37431000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:37427600-37431000	Strong transcription	Brain Angular Gyrus	brain
30	chr19:37427600-37431000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:37427600-37431000	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr19:37427600-37431200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
33	chr19:37427600-37431200	Strong transcription	Fetal Kidney	kidney
34	chr19:37427600-37431400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:37427600-37431400	Strong transcription	Brain Anterior Caudate	brain
36	chr19:37427600-37432000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr19:37427600-37432000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:37427600-37432400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:37427600-37432600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr19:37427600-37432800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr19:37427600-37432800	Strong transcription	NHDF-Ad	bronchial
42	chr19:37427600-37436800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr19:37427800-37431600	Strong transcription	Brain Cingulate Gyrus	brain
44	chr19:37427800-37432000	Strong transcription	Placenta	Placenta
45	chr19:37427800-37434400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:37428000-37431000	Strong transcription	NH-A	brain
47	chr19:37428000-37431600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr19:37428000-37432000	Strong transcription	Primary B cells from cord blood	blood
49	chr19:37428200-37430800	Strong transcription	Psoas Muscle	Psoas
50	chr19:37428200-37431000	Weak transcription	NHLF	lung

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