Variant report

Variant	rs3108566
Chromosome Location	chr19:37195824-37195825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10402486	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10407386	0.98[EUR][1000 genomes]
rs10409630	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11084862	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11669642	0.88[ASN][1000 genomes]
rs11672680	0.88[ASN][1000 genomes]
rs12610353	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830031	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2033077	0.86[EUR][1000 genomes]
rs2217081	0.82[EUR][1000 genomes]
rs2385564	0.87[ASN][1000 genomes]
rs2385642	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2385643	0.86[EUR][1000 genomes]
rs3096617	0.85[EUR][1000 genomes]
rs3096618	0.85[EUR][1000 genomes]
rs3096619	0.85[EUR][1000 genomes]
rs3096622	0.86[EUR][1000 genomes]
rs3096623	0.86[EUR][1000 genomes]
rs3096627	0.86[EUR][1000 genomes]
rs3096628	0.86[EUR][1000 genomes]
rs3096630	0.86[EUR][1000 genomes]
rs3096631	0.85[EUR][1000 genomes]
rs3096632	0.86[EUR][1000 genomes]
rs3096633	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3096636	0.87[EUR][1000 genomes]
rs3108166	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108167	0.88[EUR][1000 genomes]
rs3108168	0.88[EUR][1000 genomes]
rs3108171	0.87[EUR][1000 genomes]
rs3108172	0.87[EUR][1000 genomes]
rs3108174	0.88[EUR][1000 genomes]
rs3108179	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108181	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108182	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108184	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108185	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108186	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108187	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108188	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108189	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108190	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108191	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108192	0.81[EUR][1000 genomes]
rs3108193	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108196	0.81[ASN][1000 genomes]
rs3108197	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108201	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108203	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108205	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108206	0.84[EUR][1000 genomes]
rs3108208	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108209	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108212	0.82[ASN][1000 genomes]
rs3108214	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108215	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108218	0.88[ASN][1000 genomes]
rs3108219	0.88[ASN][1000 genomes]
rs3108542	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108543	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108544	0.90[EUR][1000 genomes]
rs3108545	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108546	0.90[EUR][1000 genomes]
rs3108549	0.81[ASN][1000 genomes]
rs3108550	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108552	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108555	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108559	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108560	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108562	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108563	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108564	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108565	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108567	0.85[EUR][1000 genomes]
rs3108568	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108570	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108572	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108573	0.88[ASN][1000 genomes]
rs3108574	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108575	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108576	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108577	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108579	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108580	0.85[EUR][1000 genomes]
rs3108583	0.88[ASN][1000 genomes]
rs3108585	0.88[ASN][1000 genomes]
rs3108589	0.88[ASN][1000 genomes]
rs3108590	0.88[ASN][1000 genomes]
rs3108591	0.84[ASN][1000 genomes]
rs3108592	0.95[ASN][1000 genomes]
rs3108594	0.86[EUR][1000 genomes]
rs3108596	0.86[EUR][1000 genomes]
rs3108597	0.85[EUR][1000 genomes]
rs3108600	0.85[EUR][1000 genomes]
rs3108602	0.85[EUR][1000 genomes]
rs3108603	0.86[EUR][1000 genomes]
rs3108604	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108607	0.88[EUR][1000 genomes]
rs3108608	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108609	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3108610	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3111541	0.85[EUR][1000 genomes]
rs3111547	0.86[EUR][1000 genomes]
rs3111549	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3111550	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34002069	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34395293	0.85[EUR][1000 genomes]
rs4507019	0.86[EUR][1000 genomes]
rs4572520	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4806336	0.86[EUR][1000 genomes]
rs7245414	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7248477	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7250376	0.88[ASN][1000 genomes]
rs7252957	0.97[EUR][1000 genomes]
rs7256786	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7259195	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7259256	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8105197	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS 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	27 gene(s)	inside rSNPs	diseases
8	esv3420176	chr19:37130161-37207917	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
9	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv470139	chr19:37171201-37264190	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv3517005	chr19:37193712-37364110	Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	esv3517004	chr19:37193762-37363960	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	esv3517006	chr19:37193762-37363960	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3108566	AC092295.7	cis	Esophagus Muscularis	GTEx
rs3108566	ZNF567	Cis_1M	lymphoblastoid	RTeQTL
rs3108566	AC074138.3	cis	Thyroid	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37179400-37199200	Weak transcription	Fetal Heart	heart
2	chr19:37183600-37203200	Weak transcription	K562	blood
3	chr19:37184400-37199000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:37187600-37196800	Weak transcription	Brain Angular Gyrus	brain
5	chr19:37187600-37198400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:37188000-37196400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:37188400-37197000	Weak transcription	Fetal Kidney	kidney
8	chr19:37194000-37254000	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr19:37194400-37211600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
10	chr19:37194400-37213400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
11	chr19:37194400-37214400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr19:37194400-37214600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr19:37194400-37215600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:37194400-37219400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
15	chr19:37194400-37221400	ZNF genes & repeats	Dnd41	blood
16	chr19:37194400-37253800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:37194600-37196600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:37194600-37197800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:37194600-37197800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
20	chr19:37194600-37204400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:37194600-37211400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr19:37194600-37211800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
23	chr19:37194600-37212000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:37194600-37213000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr19:37194600-37214400	ZNF genes & repeats	A549	lung
26	chr19:37194600-37214600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
27	chr19:37194600-37214800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr19:37194600-37215000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:37194600-37215200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:37194600-37220800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
31	chr19:37194600-37227000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr19:37194600-37258800	ZNF genes & repeats	Liver	Liver
33	chr19:37194800-37196400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:37194800-37197000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr19:37194800-37214600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
36	chr19:37195000-37196600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:37195000-37197000	Weak transcription	Gastric	stomach
38	chr19:37195000-37197000	Weak transcription	Pancreas	Pancrea
39	chr19:37195400-37196400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr19:37195400-37196800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:37195400-37196800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:37195400-37196800	Weak transcription	Fetal Intestine Small	intestine
43	chr19:37195400-37196800	Weak transcription	Thymus	Thymus
44	chr19:37195400-37197000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:37195400-37197000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:37195400-37197000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:37195400-37197000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:37195400-37197000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:37195400-37197000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:37195400-37197000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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