Variant report

Variant	rs55778393
Chromosome Location	chr19:21770143-21770144
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:21769002-21771379	PBDE	blood:	n/a	n/a
2	SIN3A	chr19:21769268-21770569	H1-hESC	embryonic stem cell:	n/a	chr19:21769374-21769387 chr19:21769326-21769339 chr19:21769482-21769493

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF100-2	chr19:21769665-21770179	NONHSAT063726

Variant related genes	Relation type
ENSG00000268555	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 42 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10854054	0.83[ASN][1000 genomes]
rs11085469	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11667151	0.86[ASN][1000 genomes]
rs11879044	0.93[ASN][1000 genomes]
rs11881160	0.81[ASN][1000 genomes]
rs11881176	0.81[ASN][1000 genomes]
rs12327638	0.81[EUR][1000 genomes]
rs12459715	0.85[ASN][1000 genomes]
rs12608625	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12610221	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12972148	0.93[ASN][1000 genomes]
rs12973203	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12973209	0.85[ASN][1000 genomes]
rs12974817	0.93[ASN][1000 genomes]
rs12979255	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12981277	0.87[ASN][1000 genomes]
rs1520068	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1520069	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1520070	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1533674	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1850937	0.85[ASN][1000 genomes]
rs2102920	0.93[ASN][1000 genomes]
rs2102922	0.85[ASN][1000 genomes]
rs2139530	0.85[ASN][1000 genomes]
rs2359157	0.85[ASN][1000 genomes]
rs34692125	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34835488	0.93[ASN][1000 genomes]
rs35092215	0.82[ASN][1000 genomes]
rs35229762	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35465051	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35998933	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3817397	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4809140	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4809141	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4809146	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4809147	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4809148	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4809151	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4809152	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4809153	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57229007	0.83[ASN][1000 genomes]
rs59054166	0.93[ASN][1000 genomes]
rs61137407	0.83[ASN][1000 genomes]
rs62110244	0.93[ASN][1000 genomes]
rs62110249	0.83[ASN][1000 genomes]
rs6511268	0.83[EUR][1000 genomes]
rs6511273	0.84[ASN][1000 genomes]
rs67854708	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67876192	0.82[EUR][1000 genomes]
rs68172713	0.85[AFR][1000 genomes]
rs7246154	0.85[ASN][1000 genomes]
rs7248367	0.85[ASN][1000 genomes]
rs7250457	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250470	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250663	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250960	0.86[ASN][1000 genomes]
rs7251111	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7254018	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7254378	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255081	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7257246	0.85[ASN][1000 genomes]
rs7260514	0.85[ASN][1000 genomes]
rs8109757	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8110320	0.85[ASN][1000 genomes]
rs8111076	0.85[ASN][1000 genomes]
rs8111313	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112158	0.85[ASN][1000 genomes]
rs8112960	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9749033	0.85[ASN][1000 genomes]
rs9749043	0.85[ASN][1000 genomes]
rs9749067	0.84[ASN][1000 genomes]
rs9749163	0.85[ASN][1000 genomes]
rs9749167	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1056332	chr19:21746555-21807647	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv543947	chr19:21749857-21772586	Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv543948	chr19:21763457-21775948	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
10	nsv960938	chr19:21766627-21785276	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:42)

SNP	Gene	Cis/trans	Tissue	Source
rs55778393	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs55778393	RP11-678G14.4	cis	Muscle Skeletal	GTEx
rs55778393	CTD-2561J22.5	cis	Esophagus Mucosa	GTEx
rs55778393	ZNF429	cis	lung	GTEx
rs55778393	RP11-678G14.3	cis	Whole Blood	GTEx
rs55778393	RP11-678G14.3	cis	Artery Aorta	GTEx
rs55778393	CTD-2561J22.5	cis	Thyroid	GTEx
rs55778393	ZNF429	cis	Esophagus Mucosa	GTEx
rs55778393	CTD-2561J22.5	cis	lung	GTEx
rs55778393	LOC400680	Cis_1M	lymphoblastoid	RTeQTL
rs55778393	CTD-2626G11.2	cis	Skin Sun Exposed Lower leg	GTEx
rs55778393	LINC00664	cis	Muscle Skeletal	GTEx
rs55778393	ZNF493	cis	Whole Blood	GTEx
rs55778393	LINC00664	cis	Whole Blood	GTEx
rs55778393	RP11-420K14.1	cis	Muscle Skeletal	GTEx
rs55778393	ZNF429	cis	Skin Sun Exposed Lower leg	GTEx
rs55778393	LINC00664	cis	Esophagus Mucosa	GTEx
rs55778393	RP11-678G14.2	cis	Thyroid	GTEx
rs55778393	CTD-2561J22.5	cis	Whole Blood	GTEx
rs55778393	RP11-678G14.2	cis	Whole Blood	GTEx
rs55778393	RP11-678G14.3	cis	Stomach	GTEx
rs55778393	RP11-420K14.2	cis	Whole Blood	GTEx
rs55778393	RP11-420K14.2	cis	lung	GTEx
rs55778393	RP11-420K14.2	cis	Heart Left Ventricle	GTEx
rs55778393	ZNF429	cis	Whole Blood	GTEx
rs55778393	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs55778393	LINC00664	cis	lung	GTEx
rs55778393	ZNF429	cis	Muscle Skeletal	GTEx
rs55778393	RP11-678G14.2	cis	Muscle Skeletal	GTEx
rs55778393	ZNF708	cis	Whole Blood	GTEx
rs55778393	RP11-678G14.3	cis	Esophagus Mucosa	GTEx
rs55778393	RP11-678G14.3	cis	lung	GTEx
rs55778393	ZNF429	cis	Artery Tibial	GTEx
rs55778393	ZNF100	cis	Muscle Skeletal	GTEx
rs55778393	ZNF43	cis	Esophagus Mucosa	GTEx
rs55778393	CTD-2561J22.5	cis	Artery Tibial	GTEx
rs55778393	RP11-678G14.2	cis	lung	GTEx
rs55778393	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs55778393	RP11-678G14.3	cis	Thyroid	GTEx
rs55778393	ZNF493	cis	Esophagus Mucosa	GTEx
rs55778393	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs55778393	RP11-678G14.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21766200-21770600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:21767600-21770800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr19:21767800-21770800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:21767800-21771000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:21768000-21770600	Active TSS	Rectal Smooth Muscle	rectum
6	chr19:21768200-21770600	Active TSS	Fetal Intestine Large	intestine
7	chr19:21768400-21770200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr19:21768400-21770200	Bivalent/Poised TSS	Fetal Stomach	stomach
9	chr19:21768400-21770600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr19:21768600-21770400	Active TSS	Pancreas	Pancrea
11	chr19:21768600-21770600	Active TSS	Fetal Intestine Small	intestine
12	chr19:21769000-21770200	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr19:21769000-21770200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr19:21769000-21770200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr19:21769000-21770200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr19:21769000-21770200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr19:21769000-21770200	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr19:21769000-21770200	Active TSS	Fetal Kidney	kidney
19	chr19:21769000-21770200	Active TSS	Psoas Muscle	Psoas
20	chr19:21769000-21770200	Active TSS	Right Atrium	heart
21	chr19:21769000-21770200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr19:21769000-21770600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:21769200-21770200	Active TSS	Colon Smooth Muscle	Colon
24	chr19:21769200-21770400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:21769200-21770600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr19:21769200-21771000	Active TSS	Stomach Smooth Muscle	stomach
27	chr19:21769400-21771200	Active TSS	Colonic Mucosa	Colon
28	chr19:21769400-21771200	Transcr. at gene 5' and 3'	Dnd41	blood
29	chr19:21769600-21770200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
30	chr19:21769600-21770200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:21769600-21770200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
32	chr19:21769600-21770600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:21769600-21770600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
34	chr19:21769600-21770800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:21769600-21771400	ZNF genes & repeats	Lung	lung
36	chr19:21769800-21770200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:21769800-21770200	Active TSS	Right Ventricle	heart
38	chr19:21769800-21770200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
39	chr19:21769800-21770400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr19:21769800-21770600	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr19:21770000-21770200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr19:21770000-21770200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr19:21770000-21770200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:21770000-21770200	Active TSS	Brain Germinal Matrix	brain
45	chr19:21770000-21770200	Enhancers	Placenta	Placenta
46	chr19:21770000-21770200	Active TSS	Left Ventricle	heart
47	chr19:21770000-21770200	Flanking Active TSS	Ovary	ovary
48	chr19:21770000-21770400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:21770000-21770400	Weak transcription	Fetal Heart	heart
50	chr19:21770000-21770400	Active TSS	Skeletal Muscle Female	skeletal muscle

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