Variant report

Variant	rs256740
Chromosome Location	chr19:37856353-37856354
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	chr19:37855409..37858293-chr19:37876540..37879521,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1019494	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10419281	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10425719	0.96[JPT][hapmap]
rs11083420	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11083423	0.83[ASN][1000 genomes]
rs11666708	0.94[ASN][1000 genomes]
rs12462487	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12462708	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1545755	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17244713	0.89[CEU][hapmap]
rs17244769	0.87[CEU][hapmap]
rs17303902	0.88[CEU][hapmap]
rs185368	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs185369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1968251	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs2385180	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2385181	0.94[ASN][1000 genomes]
rs2431992	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs256733	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs256735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs256744	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs320881	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs4344867	0.81[ASN][1000 genomes]
rs502546	0.93[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55755939	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55926714	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508721	0.87[ASN][1000 genomes]
rs7254009	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs73025481	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109103	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs862234	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs256740	AC012309.5	cis	Thyroid	GTEx
rs256740	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs256740	HKR1	cis	Whole Blood	GTEx
rs256740	AC012309.5	cis	Muscle Skeletal	GTEx
rs256740	AC012309.5	cis	Esophagus Mucosa	GTEx
rs256740	AC012309.5	cis	Nerve Tibial	GTEx
rs256740	AC012309.5	cis	Artery Tibial	GTEx
rs256740	AC012309.5	cis	lung	GTEx
rs256740	AC012309.5	cis	Esophagus Muscularis	GTEx
rs256740	ZNF781	cis	Thyroid	GTEx
rs256740	AC012309.5	cis	Heart Left Ventricle	GTEx
rs256740	AC012309.5	cis	Adipose Subcutaneous	GTEx
rs256740	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37826600-37861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:37842800-37856600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:37843800-37857600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:37844000-37857000	ZNF genes & repeats	Liver	Liver
5	chr19:37846200-37856400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:37849200-37857000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:37850000-37856800	ZNF genes & repeats	A549	lung
8	chr19:37851000-37856400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:37851000-37856600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr19:37852200-37857000	ZNF genes & repeats	Dnd41	blood
11	chr19:37853000-37856600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr19:37853000-37856600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
13	chr19:37853000-37857000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
14	chr19:37853200-37856400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:37853200-37856800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
16	chr19:37853200-37857000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:37853200-37857200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:37853400-37856600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:37853600-37856600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr19:37854200-37857000	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr19:37854200-37861200	Weak transcription	Psoas Muscle	Psoas
22	chr19:37854200-37861400	Weak transcription	Small Intestine	intestine
23	chr19:37855000-37861400	Weak transcription	Fetal Heart	heart
24	chr19:37855000-37861600	Weak transcription	Aorta	Aorta
25	chr19:37855200-37856400	ZNF genes & repeats	HepG2	liver
26	chr19:37855200-37860800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:37855200-37861000	Weak transcription	Right Ventricle	heart
28	chr19:37855200-37861200	Weak transcription	Left Ventricle	heart
29	chr19:37855200-37861400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:37855200-37861400	Weak transcription	Fetal Brain Male	brain
31	chr19:37855200-37861400	Weak transcription	NH-A	brain
32	chr19:37855400-37856400	ZNF genes & repeats	Brain Hippocampus Middle	brain
33	chr19:37855400-37860400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr19:37855400-37860800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:37855400-37860800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:37855400-37861000	Weak transcription	Fetal Kidney	kidney
37	chr19:37855400-37861400	Weak transcription	Hela-S3	cervix
38	chr19:37855600-37860600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr19:37855600-37860800	Weak transcription	Brain Angular Gyrus	brain
40	chr19:37855600-37861200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:37855600-37861200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr19:37855600-37861400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr19:37855600-37861400	Weak transcription	Ovary	ovary
44	chr19:37855600-37861400	Weak transcription	HSMMtube	muscle
45	chr19:37855600-37861400	Weak transcription	Osteobl	bone
46	chr19:37855800-37860800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:37855800-37861200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:37855800-37861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:37855800-37861400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr19:37856000-37856800	ZNF genes & repeats	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links