Variant report

Variant	rs573294
Chromosome Location	chr19:37410162-37410163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11667146	1.00[JPT][hapmap]
rs1644638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1644645	1.00[JPT][hapmap]
rs1644710	1.00[ASN][1000 genomes]
rs1644711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1667384	1.00[ASN][1000 genomes]
rs1726719	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1726724	0.87[AFR][1000 genomes]
rs2551047	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35011739	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3745768	1.00[JPT][hapmap]
rs3745770	1.00[JPT][hapmap]
rs476194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484001	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs485034	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs491326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494804	0.84[ASN][1000 genomes]
rs496872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs505717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs508361	0.80[AFR][1000 genomes]
rs510214	1.00[CHB][hapmap];0.87[YRI][hapmap]
rs510757	1.00[ASW][hapmap];0.89[AFR][1000 genomes]
rs513406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs517110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs519606	1.00[CHB][hapmap];0.87[YRI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs540451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[ASN][1000 genomes]
rs544543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs547483	0.88[ASW][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs551717	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs563786	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567796	0.90[ASN][1000 genomes]
rs568654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs578655	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580846	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs8108727	1.00[JPT][hapmap]
rs826262	1.00[ASW][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs826289	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs826290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs826294	0.90[ASN][1000 genomes]
rs826296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs826303	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs826304	0.88[ASW][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[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	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription 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	12 gene(s)	inside rSNPs	diseases
14	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
15	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
16	nsv458569	chr19:37331614-37412887	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv579462	chr19:37331614-37412887	Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
18	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs573294	ZNF260	cis	Esophagus Mucosa	GTEx
rs573294	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs573294	AC012309.5	cis	Thyroid	GTEx
rs573294	AC012309.5	cis	Esophagus Mucosa	GTEx
rs573294	ZNF585B	cis	Artery Tibial	GTEx
rs573294	AC012309.5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37408000-37410800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:37408200-37410200	Weak transcription	Pancreas	Pancrea
3	chr19:37408200-37410200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:37408200-37410400	Weak transcription	Esophagus	oesophagus
5	chr19:37408200-37413000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:37408200-37413000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:37408200-37413000	Weak transcription	Aorta	Aorta
8	chr19:37408200-37413000	Weak transcription	Colonic Mucosa	Colon
9	chr19:37408200-37436400	Weak transcription	Fetal Thymus	thymus
10	chr19:37408200-37440600	Weak transcription	Stomach Mucosa	stomach
11	chr19:37408400-37410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:37408400-37410200	Weak transcription	Fetal Stomach	stomach
13	chr19:37408400-37410200	Weak transcription	Psoas Muscle	Psoas
14	chr19:37408400-37410400	Weak transcription	Gastric	stomach
15	chr19:37408400-37411800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr19:37408400-37411800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:37408400-37412800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:37408400-37412800	Weak transcription	HUVEC	blood vessel
19	chr19:37408400-37413000	Weak transcription	Fetal Intestine Large	intestine
20	chr19:37408400-37413000	Weak transcription	Spleen	Spleen
21	chr19:37408400-37417000	Weak transcription	Fetal Kidney	kidney
22	chr19:37408400-37440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:37408600-37410200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:37408600-37410800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:37408600-37412600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:37408600-37412800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:37408600-37412800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr19:37408600-37439600	Weak transcription	Fetal Heart	heart
29	chr19:37408800-37410600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:37408800-37411000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
31	chr19:37408800-37411200	Strong transcription	Ovary	ovary
32	chr19:37408800-37414800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr19:37408800-37415200	Strong transcription	Left Ventricle	heart
34	chr19:37409000-37410200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:37409000-37410400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:37409000-37410600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:37409000-37410600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr19:37409000-37410600	Strong transcription	HSMMtube	muscle
39	chr19:37409000-37410800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr19:37409000-37410800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:37409000-37410800	ZNF genes & repeats	Liver	Liver
42	chr19:37409000-37410800	Strong transcription	Brain Germinal Matrix	brain
43	chr19:37409000-37410800	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr19:37409000-37410800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr19:37409000-37411000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr19:37409000-37412800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:37409000-37413800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:37409000-37413800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr19:37409000-37413800	Strong transcription	Fetal Muscle Leg	muscle
50	chr19:37409000-37414200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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