Variant report

Variant	rs563786
Chromosome Location	chr19:37412914-37412915
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	chr19:37405380..37408333-chr19:37412047..37415045,3	MCF-7	breast:
2	chr19:37411760..37413673-chr19:37428843..37431824,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198453	Chromatin interaction
ENSG00000185869	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1423047	0.82[AFR][1000 genomes]
rs1644638	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1644640	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1644641	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1644642	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1644643	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1644645	0.80[AFR][1000 genomes]
rs1644710	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1644711	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1667384	1.00[ASN][1000 genomes]
rs1726719	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1726724	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2547055	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2551047	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35011739	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs472226	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs474017	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs475026	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs476194	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484001	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs485034	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491326	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494804	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs496872	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs505717	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs508361	0.88[AFR][1000 genomes]
rs510757	0.97[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs513406	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs517110	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519606	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs524802	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs528504	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs529468	0.85[AFR][1000 genomes]
rs540451	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs544543	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs547483	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs551717	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs565721	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs567796	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs568654	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs569371	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs573294	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578655	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579452	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734381	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs826262	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826289	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs826290	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs826294	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs826296	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs826303	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs826304	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs826307	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs826314	0.85[AFR][1000 genomes];0.80[AMR][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	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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs563786	AC012309.5	cis	Esophagus Mucosa	GTEx
rs563786	AC012309.5	cis	Esophagus Muscularis	GTEx
rs563786	AC012309.5	cis	Thyroid	GTEx
rs563786	ZNF585B	cis	Artery Tibial	GTEx
rs563786	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37408200-37413000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:37408200-37413000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:37408200-37413000	Weak transcription	Aorta	Aorta
4	chr19:37408200-37413000	Weak transcription	Colonic Mucosa	Colon
5	chr19:37408200-37436400	Weak transcription	Fetal Thymus	thymus
6	chr19:37408200-37440600	Weak transcription	Stomach Mucosa	stomach
7	chr19:37408400-37413000	Weak transcription	Fetal Intestine Large	intestine
8	chr19:37408400-37413000	Weak transcription	Spleen	Spleen
9	chr19:37408400-37417000	Weak transcription	Fetal Kidney	kidney
10	chr19:37408400-37440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:37408600-37439600	Weak transcription	Fetal Heart	heart
12	chr19:37408800-37414800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr19:37408800-37415200	Strong transcription	Left Ventricle	heart
14	chr19:37409000-37413800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:37409000-37413800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:37409000-37413800	Strong transcription	Fetal Muscle Leg	muscle
17	chr19:37409000-37414200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:37409000-37414800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:37409000-37415000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:37409000-37444800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:37409000-37447400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:37409200-37413000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr19:37409200-37413800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr19:37409200-37413800	Strong transcription	Brain Anterior Caudate	brain
25	chr19:37409200-37414200	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr19:37409200-37414400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:37409200-37414600	Strong transcription	Fetal Lung	lung
28	chr19:37409200-37415000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:37409400-37413800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:37409400-37414000	Strong transcription	Fetal Brain Female	brain
31	chr19:37409400-37414800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr19:37409400-37415000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:37409600-37423600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:37409800-37413800	Strong transcription	Dnd41	blood
35	chr19:37409800-37416000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:37409800-37421400	Weak transcription	Fetal Brain Male	brain
37	chr19:37410000-37413000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr19:37410000-37415400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:37410200-37413800	Strong transcription	Fetal Stomach	stomach
40	chr19:37410200-37415000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:37410600-37413000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:37410600-37413000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:37410600-37413000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:37410600-37413000	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:37410600-37413000	Weak transcription	Esophagus	oesophagus
46	chr19:37410600-37413000	Weak transcription	Gastric	stomach
47	chr19:37410600-37413000	Weak transcription	Pancreas	Pancrea
48	chr19:37410600-37413000	Weak transcription	Right Ventricle	heart
49	chr19:37410600-37413200	Weak transcription	HSMMtube	muscle
50	chr19:37410600-37413400	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links