Variant report

Variant	rs256744
Chromosome Location	chr19:37855488-37855489
allele	C/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: 36 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1019494	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10419281	1.00[ASW][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs10425719	0.95[JPT][hapmap]
rs11083420	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11083423	0.83[ASN][1000 genomes]
rs11666708	0.94[ASN][1000 genomes]
rs12462487	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12462708	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1545755	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs17244713	0.88[CEU][hapmap]
rs17244769	0.86[CEU][hapmap]
rs17303902	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs185368	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs185369	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs1968251	0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2385180	0.82[ASW][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs2385181	0.94[ASN][1000 genomes]
rs2431992	0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs256733	0.82[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs256735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs256740	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs320881	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs320887	0.81[TSI][hapmap]
rs4344867	0.81[ASN][1000 genomes]
rs502546	0.92[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55755939	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55926714	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6508721	0.87[ASN][1000 genomes]
rs7254009	1.00[ASW][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs73025481	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109103	0.82[ASW][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs862234	1.00[ASW][hapmap];0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs256744	AC012309.5	cis	Nerve Tibial	GTEx
rs256744	AC012309.5	cis	Esophagus Mucosa	GTEx
rs256744	AC012309.5	cis	Muscle Skeletal	GTEx
rs256744	HKR1	cis	Whole Blood	GTEx
rs256744	AC012309.5	cis	Esophagus Muscularis	GTEx
rs256744	ZNF781	cis	Thyroid	GTEx
rs256744	AC012309.5	cis	Adipose Subcutaneous	GTEx
rs256744	AC012309.5	cis	Artery Tibial	GTEx
rs256744	AC012309.5	cis	Thyroid	GTEx
rs256744	AC012309.5	cis	lung	GTEx
rs256744	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs256744	AC012309.5	cis	Heart Left Ventricle	GTEx
rs256744	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs256744	ZNF585B	cis	Artery Tibial	GTEx

Chromatin state (count:85 , 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	chr19:37828000-37855800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:37842800-37856600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:37843800-37855800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:37843800-37857600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:37844000-37857000	ZNF genes & repeats	Liver	Liver
8	chr19:37845400-37855800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:37845600-37855800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:37846200-37856400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:37849200-37857000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:37850000-37855600	Strong transcription	Stomach Smooth Muscle	stomach
13	chr19:37850000-37856800	ZNF genes & repeats	A549	lung
14	chr19:37850200-37856000	Strong transcription	Fetal Lung	lung
15	chr19:37851000-37856400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:37851000-37856600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr19:37851600-37856000	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr19:37852000-37855800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:37852200-37855600	ZNF genes & repeats	Primary B cells from cord blood	blood
20	chr19:37852200-37855600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:37852200-37857000	ZNF genes & repeats	Dnd41	blood
22	chr19:37852400-37855600	Strong transcription	Brain Angular Gyrus	brain
23	chr19:37852400-37855600	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr19:37852400-37855800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:37853000-37855600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
26	chr19:37853000-37856200	ZNF genes & repeats	HSMM	muscle
27	chr19:37853000-37856600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr19:37853000-37856600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr19:37853000-37857000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
30	chr19:37853200-37855600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:37853200-37855600	ZNF genes & repeats	Colonic Mucosa	Colon
32	chr19:37853200-37855800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
33	chr19:37853200-37856400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:37853200-37856800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr19:37853200-37857000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:37853200-37857200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:37853400-37855600	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr19:37853400-37855600	ZNF genes & repeats	NHEK	skin
39	chr19:37853400-37856600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:37853600-37855600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
41	chr19:37853600-37855600	ZNF genes & repeats	Thymus	Thymus
42	chr19:37853600-37855800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
43	chr19:37853600-37855800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
44	chr19:37853600-37856600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
45	chr19:37853800-37855600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
46	chr19:37854000-37855600	ZNF genes & repeats	Fetal Intestine Large	intestine
47	chr19:37854000-37855800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
48	chr19:37854000-37855800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:37854200-37855800	ZNF genes & repeats	Placenta	Placenta
50	chr19:37854200-37857000	ZNF genes & repeats	Adipose Nuclei	Adipose

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