Variant report

Variant	rs256741
Chromosome Location	chr19:37855839-37855840
allele	G/T
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: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs3745764	0.87[AFR][1000 genomes]
rs6508712	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8107507	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs256741	AC012309.5	cis	Thyroid	GTEx
rs256741	AC012309.5	cis	Esophagus Muscularis	GTEx
rs256741	HKR1	cis	Whole Blood	GTEx
rs256741	AC012309.5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37826600-37856200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:37826600-37861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:37842800-37856600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:37843800-37857600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:37844000-37857000	ZNF genes & repeats	Liver	Liver
6	chr19:37846200-37856400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:37849200-37857000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:37850000-37856800	ZNF genes & repeats	A549	lung
9	chr19:37850200-37856000	Strong transcription	Fetal Lung	lung
10	chr19:37851000-37856400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:37851000-37856600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
12	chr19:37851600-37856000	ZNF genes & repeats	Fetal Intestine Small	intestine
13	chr19:37852200-37857000	ZNF genes & repeats	Dnd41	blood
14	chr19:37853000-37856200	ZNF genes & repeats	HSMM	muscle
15	chr19:37853000-37856600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr19:37853000-37856600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
17	chr19:37853000-37857000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
18	chr19:37853200-37856400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:37853200-37856800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
20	chr19:37853200-37857000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:37853200-37857200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:37853400-37856600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:37853600-37856600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
24	chr19:37854200-37857000	ZNF genes & repeats	Adipose Nuclei	Adipose
25	chr19:37854200-37861200	Weak transcription	Psoas Muscle	Psoas
26	chr19:37854200-37861400	Weak transcription	Small Intestine	intestine
27	chr19:37854400-37856200	ZNF genes & repeats	Brain Germinal Matrix	brain
28	chr19:37855000-37861400	Weak transcription	Fetal Heart	heart
29	chr19:37855000-37861600	Weak transcription	Aorta	Aorta
30	chr19:37855200-37856000	Weak transcription	Brain Substantia Nigra	brain
31	chr19:37855200-37856400	ZNF genes & repeats	HepG2	liver
32	chr19:37855200-37860800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr19:37855200-37861000	Weak transcription	Right Ventricle	heart
34	chr19:37855200-37861200	Weak transcription	Left Ventricle	heart
35	chr19:37855200-37861400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:37855200-37861400	Weak transcription	Fetal Brain Male	brain
37	chr19:37855200-37861400	Weak transcription	NH-A	brain
38	chr19:37855400-37856400	ZNF genes & repeats	Brain Hippocampus Middle	brain
39	chr19:37855400-37860400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr19:37855400-37860800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:37855400-37860800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:37855400-37861000	Weak transcription	Fetal Kidney	kidney
43	chr19:37855400-37861400	Weak transcription	Hela-S3	cervix
44	chr19:37855600-37860600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr19:37855600-37860800	Weak transcription	Brain Angular Gyrus	brain
46	chr19:37855600-37861200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:37855600-37861200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:37855600-37861400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr19:37855600-37861400	Weak transcription	Ovary	ovary
50	chr19:37855600-37861400	Weak transcription	HSMMtube	muscle

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