Variant report

Variant	rs6508725
Chromosome Location	chr19:37957296-37957297
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr19:37957279-37958814	H1-neurons	neurons:	n/a	chr19:37957909-37957923 chr19:37958297-37958317
2	ESRRA	chr19:37957183-37959053	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:37956743..37958791-chr19:38268721..38270290,2	K562	blood:
2	chr19:37955552..37960531-chr19:37996583..37998774,4	MCF-7	breast:
3	chr19:37945213..37949636-chr19:37955245..37960324,5	K562	blood:
4	chr19:37861003..37862628-chr19:37955117..37957748,2	MCF-7	breast:

Variant related genes	Relation type
ZNF570	TF binding region
ENSG00000189164	Chromatin interaction
ENSG00000266916	Chromatin interaction
ENSG00000188227	Chromatin interaction
ENSG00000196437	Chromatin interaction
ENSG00000189144	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1019494	0.84[ASN][1000 genomes]
rs10419281	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10425719	0.81[EUR][1000 genomes]
rs11083423	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11666708	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12981359	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12981830	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1545755	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs185368	0.81[EUR][1000 genomes]
rs185369	0.81[EUR][1000 genomes]
rs1968251	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2385180	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2385181	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs256733	0.81[EUR][1000 genomes]
rs256735	0.81[EUR][1000 genomes]
rs34410821	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35470250	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35864326	0.80[EUR][1000 genomes]
rs4344867	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6508721	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7247090	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7254009	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8109103	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6508725	AC012309.5	cis	Thyroid	GTEx
rs6508725	AC012309.5	cis	Heart Left Ventricle	GTEx
rs6508725	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs6508725	AC012309.5	cis	Artery Tibial	GTEx
rs6508725	AC012309.5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37946200-37957400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:37951400-37957400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:37951600-37957400	Weak transcription	Gastric	stomach
4	chr19:37954400-37957400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:37954400-37957400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:37955000-37957400	Weak transcription	Spleen	Spleen
7	chr19:37955800-37957400	Weak transcription	Lung	lung
8	chr19:37956000-37957400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:37956000-37957400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:37956000-37957400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:37956000-37957400	Weak transcription	Ovary	ovary
12	chr19:37956000-37957400	Weak transcription	Pancreas	Pancrea
13	chr19:37956200-37957400	Weak transcription	HSMMtube	muscle
14	chr19:37956200-37958400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:37956600-37957400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:37956600-37957400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr19:37956600-37958800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:37956800-37957400	Enhancers	Liver	Liver
19	chr19:37956800-37957400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:37956800-37957400	Enhancers	Fetal Heart	heart
21	chr19:37956800-37957800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr19:37956800-37958600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:37956800-37958600	Active TSS	GM12878-XiMat	blood
24	chr19:37956800-37960800	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr19:37956800-37961200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr19:37956800-37961200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr19:37956800-37961400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr19:37956800-37961400	Active TSS	NHLF	lung
29	chr19:37956800-37961600	Active TSS	Rectal Smooth Muscle	rectum
30	chr19:37957000-37957400	Enhancers	Primary B cells from cord blood	blood
31	chr19:37957000-37957400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:37957000-37957400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:37957000-37957400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr19:37957000-37957400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr19:37957000-37957400	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr19:37957000-37957400	Flanking Active TSS	Dnd41	blood
37	chr19:37957000-37957400	Flanking Active TSS	HepG2	liver
38	chr19:37957000-37957600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:37957000-37958000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr19:37957000-37958400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:37957000-37958400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:37957000-37958400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:37957000-37958400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr19:37957000-37958600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:37957000-37958600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:37957000-37958600	Active TSS	Aorta	Aorta
47	chr19:37957000-37958800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:37957000-37960600	Active TSS	Brain Angular Gyrus	brain
49	chr19:37957000-37960600	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr19:37957000-37961000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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