Variant report

Variant	rs3108565
Chromosome Location	chr19:37194767-37194768
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 132 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10402486	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10407386	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10409630	0.89[EUR][1000 genomes]
rs11084862	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11669642	0.99[ASN][1000 genomes]
rs11672680	0.99[ASN][1000 genomes]
rs12610353	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1830031	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033077	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2385564	0.97[ASN][1000 genomes]
rs2385642	0.84[EUR][1000 genomes]
rs2385643	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3096617	0.83[EUR][1000 genomes]
rs3096618	0.83[EUR][1000 genomes]
rs3096619	0.83[EUR][1000 genomes]
rs3096622	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3096623	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3096627	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3096628	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3096629	0.80[ASN][1000 genomes]
rs3096630	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3096631	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3096632	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3096633	0.83[EUR][1000 genomes]
rs3096636	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108166	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108167	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108168	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108171	0.85[EUR][1000 genomes]
rs3108172	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108174	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108179	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108181	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3108182	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108184	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108185	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108186	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108187	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108188	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108189	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108190	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108191	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108192	0.81[AFR][1000 genomes]
rs3108193	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108196	0.91[ASN][1000 genomes]
rs3108197	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108201	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108203	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108205	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108206	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3108208	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108209	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108212	0.92[ASN][1000 genomes]
rs3108214	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108215	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3108218	0.99[ASN][1000 genomes]
rs3108219	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108542	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108543	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108544	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108545	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108546	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108549	0.91[ASN][1000 genomes]
rs3108550	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108552	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108555	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108559	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108560	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108562	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108563	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108564	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3108566	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108567	0.83[EUR][1000 genomes]
rs3108568	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108570	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108572	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108573	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108574	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108575	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108576	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108577	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108579	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108580	0.83[EUR][1000 genomes]
rs3108583	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108585	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3108589	0.99[ASN][1000 genomes]
rs3108590	0.99[ASN][1000 genomes]
rs3108591	0.95[ASN][1000 genomes]
rs3108592	0.85[ASN][1000 genomes]
rs3108594	0.84[EUR][1000 genomes]
rs3108596	0.84[EUR][1000 genomes]
rs3108597	0.83[EUR][1000 genomes]
rs3108600	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108602	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108603	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108604	0.84[EUR][1000 genomes]
rs3108607	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108608	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3108609	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108610	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3111541	0.83[EUR][1000 genomes]
rs3111547	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3111549	0.83[EUR][1000 genomes]
rs3111550	0.84[EUR][1000 genomes]
rs34002069	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34395293	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4507019	0.84[EUR][1000 genomes]
rs4572520	0.84[EUR][1000 genomes]
rs4806336	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7245414	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7248477	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7250376	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7252957	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7256786	0.90[EUR][1000 genomes]
rs7259195	0.84[EUR][1000 genomes]
rs7259256	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8105197	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3108565	ZNF567	Cis_1M	lymphoblastoid	RTeQTL
rs3108565	AC092295.7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37179400-37194800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37179400-37199200	Weak transcription	Fetal Heart	heart
3	chr19:37183600-37203200	Weak transcription	K562	blood
4	chr19:37184400-37199000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:37186600-37195400	Weak transcription	Right Ventricle	heart
6	chr19:37187600-37194800	Weak transcription	Gastric	stomach
7	chr19:37187600-37196800	Weak transcription	Brain Angular Gyrus	brain
8	chr19:37187600-37198400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:37188000-37195800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr19:37188000-37196400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:37188400-37197000	Weak transcription	Fetal Kidney	kidney
12	chr19:37188800-37194800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr19:37188800-37195800	Weak transcription	Primary T cells from cord blood	blood
14	chr19:37194000-37254000	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr19:37194400-37194800	ZNF genes & repeats	Brain Anterior Caudate	brain
16	chr19:37194400-37195000	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr19:37194400-37195200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:37194400-37195200	ZNF genes & repeats	Fetal Intestine Large	intestine
19	chr19:37194400-37195400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:37194400-37195400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:37194400-37195400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:37194400-37195400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:37194400-37195400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr19:37194400-37195400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:37194400-37195400	ZNF genes & repeats	Aorta	Aorta
26	chr19:37194400-37195400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
27	chr19:37194400-37195400	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr19:37194400-37195400	ZNF genes & repeats	Fetal Stomach	stomach
29	chr19:37194400-37195400	ZNF genes & repeats	Left Ventricle	heart
30	chr19:37194400-37195400	ZNF genes & repeats	Lung	lung
31	chr19:37194400-37195400	ZNF genes & repeats	Ovary	ovary
32	chr19:37194400-37195400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
33	chr19:37194400-37195400	ZNF genes & repeats	Thymus	Thymus
34	chr19:37194400-37195400	ZNF genes & repeats	Spleen	Spleen
35	chr19:37194400-37195600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
36	chr19:37194400-37211600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
37	chr19:37194400-37213400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr19:37194400-37214400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
39	chr19:37194400-37214600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
40	chr19:37194400-37215600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:37194400-37219400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
42	chr19:37194400-37221400	ZNF genes & repeats	Dnd41	blood
43	chr19:37194400-37253800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:37194600-37194800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
45	chr19:37194600-37194800	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
46	chr19:37194600-37194800	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
47	chr19:37194600-37194800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:37194600-37194800	ZNF genes & repeats	Fetal Brain Female	brain
49	chr19:37194600-37194800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr19:37194600-37194800	ZNF genes & repeats	Fetal Thymus	thymus

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