Variant report

Variant	rs2603697
Chromosome Location	chr19:55609382-55609383
allele	C/T
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	MYC	chr19:55609316-55609659	NB4	blood:	n/a	n/a
2	POLR2A	chr19:55609123-55610750	HL-60	blood:	n/a	n/a
3	POLR2A	chr19:55609358-55609605	Hela-S3	cervix:	n/a	n/a
4	SPI1	chr19:55609109-55609733	HL-60	blood:	n/a	chr19:55609413-55609426 chr19:55609416-55609425 chr19:55609417-55609424
5	POLR2A	chr19:55609210-55610131	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55606533..55609893-chr19:55627288..55629671,4	MCF-7	breast:
2	chr19:55602817..55605063-chr19:55607847..55611978,5	K562	blood:
3	chr19:55549659..55551205-chr19:55608941..55611105,2	K562	blood:
4	chr19:55609257..55613232-chr19:55613674..55618222,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RDH13-2	chr19:55608844-55609398	NONHSAT067992

Variant related genes	Relation type
PPP1R12C	TF binding region
ENSG00000125503	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1860325	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs575144	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs667451	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv1063666	chr19:55030439-55622780	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv817874	chr19:55595687-55614923	Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv912449	chr19:55595687-55630425	Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv912450	chr19:55595687-55633043	Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv912452	chr19:55595687-55644325	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv978854	chr19:55600405-55611152	Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	esv19087	chr19:55607778-55609493	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv1794231	chr19:55608310-55609574	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2603697	RDH13	cis	Artery Aorta	GTEx
rs2603697	EPS8L1	cis	Artery Tibial	GTEx
rs2603697	RDH13	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55593800-55620400	Weak transcription	HMEC	breast
2	chr19:55599200-55626600	Weak transcription	Fetal Kidney	kidney
3	chr19:55599200-55627200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:55599400-55614800	Weak transcription	GM12878-XiMat	blood
5	chr19:55599800-55626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:55600000-55610600	Weak transcription	NHDF-Ad	bronchial
7	chr19:55600000-55612800	Weak transcription	HSMMtube	muscle
8	chr19:55600000-55613400	Weak transcription	Fetal Lung	lung
9	chr19:55600000-55613800	Weak transcription	NH-A	brain
10	chr19:55600000-55614600	Weak transcription	HSMM	muscle
11	chr19:55600000-55626600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr19:55600000-55627000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr19:55600200-55609800	Weak transcription	Stomach Mucosa	stomach
14	chr19:55600200-55610800	Strong transcription	NHLF	lung
15	chr19:55600200-55612600	Weak transcription	K562	blood
16	chr19:55600200-55614600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:55600600-55614600	Weak transcription	HUVEC	blood vessel
18	chr19:55601400-55611000	Weak transcription	Right Atrium	heart
19	chr19:55601400-55626400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:55601800-55609800	Strong transcription	Colonic Mucosa	Colon
21	chr19:55602000-55613800	Strong transcription	Gastric	stomach
22	chr19:55602000-55615400	Strong transcription	Lung	lung
23	chr19:55602000-55618400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:55602800-55614200	Weak transcription	Psoas Muscle	Psoas
25	chr19:55602800-55626400	Weak transcription	Hela-S3	cervix
26	chr19:55603600-55609400	Weak transcription	NHEK	skin
27	chr19:55603800-55612600	Weak transcription	Small Intestine	intestine
28	chr19:55605600-55610000	Strong transcription	Brain Hippocampus Middle	brain
29	chr19:55605600-55614400	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr19:55605800-55609400	Strong transcription	Right Ventricle	heart
31	chr19:55606400-55609400	Weak transcription	A549	lung
32	chr19:55606400-55613600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:55606400-55613800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr19:55606400-55621600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:55606600-55610800	Weak transcription	Fetal Heart	heart
36	chr19:55606600-55612600	Weak transcription	Brain Substantia Nigra	brain
37	chr19:55606600-55614000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:55606600-55614200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr19:55606600-55627200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr19:55606800-55609400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:55606800-55609400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:55606800-55613200	Weak transcription	Brain Angular Gyrus	brain
43	chr19:55606800-55613800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr19:55607000-55609400	Weak transcription	Dnd41	blood
45	chr19:55607000-55609600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr19:55607000-55609600	Weak transcription	Osteobl	bone
47	chr19:55607000-55613600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:55607000-55614800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:55607200-55609400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:55607200-55609600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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