Variant report

Variant	rs502546
Chromosome Location	chr19:37852690-37852691
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	chr19:37851946..37854387-chr19:37859960..37862069,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189164	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1019494	0.83[JPT][hapmap]
rs10419281	0.86[JPT][hapmap]
rs10425719	0.82[JPT][hapmap]
rs11083420	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11666708	0.86[ASN][1000 genomes]
rs12462487	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12462708	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1545755	0.87[JPT][hapmap]
rs17244713	0.81[CEU][hapmap]
rs17303902	0.81[CEU][hapmap]
rs185368	0.80[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs185369	0.85[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1968251	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2385180	0.86[JPT][hapmap]
rs2385181	0.86[ASN][1000 genomes]
rs2431992	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs256733	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs256735	0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs256740	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256744	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2921561	0.84[EUR][1000 genomes]
rs320881	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs320887	0.84[CEU][hapmap]
rs55755939	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55926714	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7254009	0.86[JPT][hapmap]
rs73025481	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109103	0.86[JPT][hapmap]
rs862234	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv9718	chr19:37839070-37852872	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs502546	AC012309.5	cis	Thyroid	GTEx
rs502546	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs502546	AC012309.5	cis	Artery Tibial	GTEx
rs502546	ZNF781	cis	Thyroid	GTEx
rs502546	AC012309.5	cis	Heart Left Ventricle	GTEx
rs502546	AC012309.5	cis	Muscle Skeletal	GTEx
rs502546	AC012309.5	cis	Esophagus Muscularis	GTEx
rs502546	AC012309.5	cis	Esophagus Mucosa	GTEx
rs502546	HKR1	cis	Whole Blood	GTEx
rs502546	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs502546	AC012309.5	cis	Nerve Tibial	GTEx
rs502546	AC012309.5	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37826200-37853200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37826600-37856200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:37826600-37861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:37826800-37853400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:37827000-37853400	Weak transcription	Stomach Mucosa	stomach
6	chr19:37828000-37855800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:37830000-37853600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:37830800-37853200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:37839000-37852800	Weak transcription	Brain Substantia Nigra	brain
10	chr19:37839600-37853200	Weak transcription	Hela-S3	cervix
11	chr19:37839800-37853600	Weak transcription	Fetal Heart	heart
12	chr19:37840400-37853200	Weak transcription	NH-A	brain
13	chr19:37840800-37853200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:37841200-37855200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:37842600-37855400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr19:37842800-37856600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:37843800-37855800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:37843800-37857600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr19:37844000-37857000	ZNF genes & repeats	Liver	Liver
20	chr19:37845400-37855800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
21	chr19:37845600-37853200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:37845600-37853600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr19:37845600-37855800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:37845800-37853000	Weak transcription	NHLF	lung
25	chr19:37846200-37853200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:37846200-37856400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:37846400-37854600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
28	chr19:37846600-37853600	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:37847000-37852800	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr19:37847000-37854200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:37847600-37852800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:37847600-37852800	ZNF genes & repeats	Fetal Intestine Large	intestine
33	chr19:37847800-37852800	Weak transcription	Fetal Brain Male	brain
34	chr19:37847800-37853000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:37847800-37854800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:37848000-37853400	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr19:37848000-37853600	Weak transcription	Psoas Muscle	Psoas
38	chr19:37848200-37853200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr19:37848200-37854400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr19:37848200-37855200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr19:37848400-37853400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:37848600-37853200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr19:37848600-37854400	Strong transcription	Fetal Muscle Leg	muscle
44	chr19:37848600-37855200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr19:37848800-37853200	Strong transcription	Ovary	ovary
46	chr19:37849000-37853600	Strong transcription	Primary T cells from cord blood	blood
47	chr19:37849000-37854600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
48	chr19:37849000-37854800	Strong transcription	Fetal Stomach	stomach
49	chr19:37849200-37857000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:37849400-37853000	Strong transcription	Duodenum Smooth Muscle	Duodenum

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