Variant report

Variant	rs58192477
Chromosome Location	chr19:36849843-36849844
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	chr19:36848342..36851339-chr19:37018243..37021228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228629	Chromatin interaction
ENSG00000254004	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10418925	0.83[ASN][1000 genomes]
rs11084855	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11084857	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1127406	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1129375	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1129376	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11882601	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11882671	0.87[AFR][1000 genomes]
rs17206365	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17639740	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2918350	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2918352	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2918353	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2918354	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2918362	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2918363	0.83[ASN][1000 genomes]
rs2918366	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918367	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2918371	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2918374	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967485	0.81[ASN][1000 genomes]
rs2967486	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2967487	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2967488	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2967490	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967491	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967492	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2967494	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967495	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967498	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967499	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967502	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967503	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2972630	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2972634	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972635	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972636	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972637	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2972638	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2972643	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972650	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972654	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972655	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34723481	0.83[ASN][1000 genomes]
rs35007948	0.81[ASN][1000 genomes]
rs35822095	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57488812	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58333554	0.80[EUR][1000 genomes]
rs60499535	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60842204	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61055798	0.81[AFR][1000 genomes]
rs62112620	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62112621	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62112627	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112629	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62112634	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73043854	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7343105	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8111845	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8113638	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2474	chr19:36804469-36865415	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1064343	chr19:36807288-36853102	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1066190	chr19:36830299-36852877	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv174	chr19:36831719-36865415	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv9716	chr19:36840250-36851177	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv579459	chr19:36845537-36856379	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv579460	chr19:36846000-36850222	Weak transcription ZNF genes & repeats Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1795509	chr19:36847366-36852733	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58192477	LOC284412	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36823800-36853600	ZNF genes & repeats	Liver	Liver
2	chr19:36827200-36862200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:36830600-36869400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:36832200-36868600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:36832400-36851400	Weak transcription	Fetal Brain Male	brain
6	chr19:36834000-36857400	Weak transcription	Brain Substantia Nigra	brain
7	chr19:36834200-36868800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:36835800-36857200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:36835800-36868800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:36836400-36858400	Weak transcription	Osteobl	bone
11	chr19:36836400-36868000	Weak transcription	Psoas Muscle	Psoas
12	chr19:36836600-36857200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:36836600-36863400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:36837000-36852600	Strong transcription	Fetal Stomach	stomach
15	chr19:36838000-36851200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:36838000-36851200	Weak transcription	HepG2	liver
17	chr19:36838000-36868600	Weak transcription	Stomach Mucosa	stomach
18	chr19:36838200-36855000	Weak transcription	HSMM	muscle
19	chr19:36838600-36850400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:36839400-36851200	Weak transcription	HSMMtube	muscle
21	chr19:36839800-36850600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:36839800-36851200	Weak transcription	Placenta	Placenta
23	chr19:36840000-36855000	Weak transcription	Right Ventricle	heart
24	chr19:36840000-36856000	Weak transcription	Fetal Lung	lung
25	chr19:36841200-36854800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:36842400-36861200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:36842600-36851600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr19:36843600-36851000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:36844200-36851000	Weak transcription	Fetal Kidney	kidney
30	chr19:36844200-36868800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:36844600-36850400	Weak transcription	Fetal Intestine Large	intestine
32	chr19:36845200-36853000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:36845200-36853200	Strong transcription	Adipose Nuclei	Adipose
34	chr19:36845200-36858200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:36845600-36853200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:36845600-36853200	Strong transcription	Brain Germinal Matrix	brain
37	chr19:36845800-36859200	Weak transcription	Fetal Thymus	thymus
38	chr19:36846000-36853200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr19:36846000-36855000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:36846200-36852600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:36846600-36851400	Strong transcription	Primary B cells from cord blood	blood
42	chr19:36846600-36866400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:36847000-36853400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:36847200-36851200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr19:36847200-36852600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:36847200-36853200	Strong transcription	Brain Angular Gyrus	brain
47	chr19:36847200-36853200	Strong transcription	Thymus	Thymus
48	chr19:36847200-36853400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:36847200-36853600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
50	chr19:36847200-36859200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links