Variant report

Variant	rs2358609
Chromosome Location	chr19:21113503-21113504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10404578	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10405567	0.82[EUR][1000 genomes]
rs10409571	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10411595	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10419370	0.82[EUR][1000 genomes]
rs10419799	0.82[EUR][1000 genomes]
rs10419820	0.82[EUR][1000 genomes]
rs10424164	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10426262	0.84[ASN][1000 genomes]
rs11085399	0.98[ASN][1000 genomes]
rs11085400	0.98[ASN][1000 genomes]
rs11085401	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12463381	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12608830	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12973017	1.00[ASN][1000 genomes]
rs12981973	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974808	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2059140	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2161459	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2161462	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2545173	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2545221	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2545229	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2547127	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2547161	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2547162	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2547173	0.81[ASN][1000 genomes]
rs2547174	0.81[EUR][1000 genomes]
rs2547181	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs366654	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs429951	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs431157	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs439388	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4809117	0.98[ASN][1000 genomes]
rs4809118	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622661	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs625998	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs645200	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7247368	0.82[EUR][1000 genomes]
rs7250207	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7254973	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256449	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257140	0.98[ASN][1000 genomes]
rs7257497	0.83[ASN][1000 genomes]
rs7258122	0.98[ASN][1000 genomes]
rs7507539	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8099975	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8100986	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8113412	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752729	chr19:20818886-21169554	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1062776	chr19:20818886-21273361	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking 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	32 gene(s)	inside rSNPs	diseases
3	nsv932110	chr19:20818886-21278952	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS 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	32 gene(s)	inside rSNPs	diseases
4	esv2763043	chr19:20818886-21290543	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1063954	chr19:21000562-21177577	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv578946	chr19:21014403-21151796	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
8	nsv960809	chr19:21031718-21121801	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS 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	25 gene(s)	inside rSNPs	diseases
10	nsv1067455	chr19:21053665-21141787	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv1058430	chr19:21063759-21114796	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv1850387	chr19:21109758-21294264	Active TSS ZNF genes & repeats Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2358609	ZNF85	Cis_1M	lymphoblastoid	RTeQTL
rs2358609	ZNF85	cis	Stomach	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21106600-21117800	Weak transcription	Small Intestine	intestine
2	chr19:21106600-21119200	Weak transcription	Spleen	Spleen
3	chr19:21106600-21129800	Weak transcription	Stomach Mucosa	stomach
4	chr19:21106800-21119200	Weak transcription	Aorta	Aorta
5	chr19:21106800-21125600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr19:21106800-21128200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:21106800-21131000	Weak transcription	Gastric	stomach
8	chr19:21107000-21115600	Weak transcription	Pancreas	Pancrea
9	chr19:21107000-21116600	Weak transcription	Fetal Intestine Large	intestine
10	chr19:21107000-21117800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:21107000-21117800	Weak transcription	Placenta	Placenta
12	chr19:21107000-21118000	Weak transcription	Left Ventricle	heart
13	chr19:21107000-21119200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:21107000-21120400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr19:21107000-21123000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:21107000-21124000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:21107000-21125800	Weak transcription	Psoas Muscle	Psoas
18	chr19:21107000-21128000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr19:21107000-21133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:21107200-21113800	Weak transcription	Primary T cells from cord blood	blood
21	chr19:21107200-21117800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr19:21107200-21119000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:21107200-21119200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:21107200-21123000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr19:21107200-21124000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:21107200-21125400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:21107200-21127200	Weak transcription	Brain Angular Gyrus	brain
28	chr19:21107200-21127400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr19:21107200-21132600	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:21107200-21133800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:21107400-21114000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:21107400-21117800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr19:21107400-21117800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr19:21107400-21117800	Weak transcription	NHEK	skin
35	chr19:21107400-21118000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:21107400-21118000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr19:21107400-21118000	Weak transcription	Adipose Nuclei	Adipose
38	chr19:21107400-21118400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:21107400-21125600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr19:21107400-21125600	Weak transcription	HUVEC	blood vessel
41	chr19:21107400-21128000	Weak transcription	NHDF-Ad	bronchial
42	chr19:21107400-21131600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr19:21107600-21114800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:21107600-21117000	Weak transcription	Fetal Lung	lung
45	chr19:21107600-21117800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:21107600-21127000	Weak transcription	Fetal Kidney	kidney
47	chr19:21107600-21133400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:21107800-21120600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr19:21108000-21114000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:21108000-21117600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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