Variant report

Variant	rs256735
Chromosome Location	chr19:37866043-37866044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1019494	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10419281	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10425719	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs11083420	0.88[ASN][1000 genomes]
rs11083423	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11666708	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12462487	0.87[ASN][1000 genomes]
rs12462708	0.84[ASN][1000 genomes]
rs1545755	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs185368	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs185369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1968251	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2161520	0.82[JPT][hapmap]
rs2385180	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2385181	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2431992	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs256733	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256740	0.99[ASN][1000 genomes]
rs256744	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs320881	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs35470250	0.80[EUR][1000 genomes]
rs4344867	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs502546	0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs55755939	0.96[ASN][1000 genomes]
rs55926714	0.85[ASN][1000 genomes]
rs6508721	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6508725	0.81[EUR][1000 genomes]
rs7254009	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73025481	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs8109103	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs862234	0.85[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv1058788	chr19:37857748-37899157	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv579464	chr19:37858660-37881556	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs256735	AC012309.5	cis	Thyroid	GTEx
rs256735	AC012309.5	cis	Esophagus Muscularis	GTEx
rs256735	AC012309.5	cis	Heart Left Ventricle	GTEx
rs256735	AC012309.5	cis	Artery Tibial	GTEx
rs256735	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37862200-37867200	ZNF genes & repeats	A549	lung
2	chr19:37862600-37866600	Weak transcription	Gastric	stomach
3	chr19:37862600-37866600	Weak transcription	Stomach Mucosa	stomach
4	chr19:37862600-37871000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:37862800-37866400	Weak transcription	Spleen	Spleen
6	chr19:37862800-37866600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:37862800-37866600	Weak transcription	HSMMtube	muscle
8	chr19:37862800-37870600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:37862800-37871000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:37863200-37872000	Weak transcription	Fetal Heart	heart
11	chr19:37863400-37867200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:37863400-37872000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:37863600-37867000	ZNF genes & repeats	Dnd41	blood
14	chr19:37863800-37867200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:37863800-37868800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:37863800-37873200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:37864000-37866600	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr19:37864000-37867000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:37864000-37867000	ZNF genes & repeats	Primary B cells from cord blood	blood
20	chr19:37864000-37867200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
21	chr19:37864000-37867600	ZNF genes & repeats	Fetal Brain Female	brain
22	chr19:37864000-37869000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:37864000-37869400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:37864000-37882000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:37864000-37882000	ZNF genes & repeats	Liver	Liver
26	chr19:37864400-37867000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
27	chr19:37864400-37869000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
28	chr19:37864400-37869200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr19:37864400-37880600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:37864400-37880800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr19:37864600-37866600	ZNF genes & repeats	Left Ventricle	heart
32	chr19:37864600-37866800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:37864600-37867000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
34	chr19:37864600-37867000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
35	chr19:37864600-37867200	ZNF genes & repeats	Aorta	Aorta
36	chr19:37864600-37867200	ZNF genes & repeats	Brain Germinal Matrix	brain
37	chr19:37864600-37867200	ZNF genes & repeats	Pancreas	Pancrea
38	chr19:37864600-37867200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
39	chr19:37864600-37867400	ZNF genes & repeats	Thymus	Thymus
40	chr19:37864600-37867800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:37864600-37868800	ZNF genes & repeats	Ovary	ovary
42	chr19:37864600-37869200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:37864600-37873400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:37864600-37880600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
45	chr19:37864600-37890600	ZNF genes & repeats	Adipose Nuclei	Adipose
46	chr19:37864800-37866400	Strong transcription	Fetal Lung	lung
47	chr19:37864800-37866800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:37864800-37867600	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr19:37864800-37870800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr19:37864800-37870800	Strong transcription	Skeletal Muscle Male	skeletal muscle

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