Variant report

Variant	rs55755939
Chromosome Location	chr19:37844625-37844626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10419281	0.82[ASN][1000 genomes]
rs11083420	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083423	0.80[ASN][1000 genomes]
rs11666708	0.91[ASN][1000 genomes]
rs12462487	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12462708	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs185368	0.96[ASN][1000 genomes]
rs185369	0.96[ASN][1000 genomes]
rs1968251	0.82[ASN][1000 genomes]
rs2385180	0.82[ASN][1000 genomes]
rs2385181	0.91[ASN][1000 genomes]
rs2431992	0.93[ASN][1000 genomes]
rs256733	0.96[ASN][1000 genomes]
rs256735	0.96[ASN][1000 genomes]
rs256740	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256744	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2921561	0.85[EUR][1000 genomes]
rs502546	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55926714	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6508721	0.84[ASN][1000 genomes]
rs7254009	0.82[ASN][1000 genomes]
rs7257354	0.80[EUR][1000 genomes]
rs73025481	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs55755939	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs55755939	AC012309.5	cis	Esophagus Muscularis	GTEx
rs55755939	AC012309.5	cis	Muscle Skeletal	GTEx
rs55755939	ZNF781	cis	Thyroid	GTEx
rs55755939	AC012309.5	cis	Thyroid	GTEx
rs55755939	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs55755939	HKR1	cis	Whole Blood	GTEx
rs55755939	AC012309.5	cis	Artery Tibial	GTEx
rs55755939	AC012309.5	cis	Heart Left Ventricle	GTEx
rs55755939	AC012309.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 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	chr19:37826600-37848800	Weak transcription	Small Intestine	intestine
3	chr19:37826600-37856200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:37826600-37861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:37826800-37846600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:37826800-37847000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:37826800-37852600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:37826800-37853400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:37827000-37845800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:37827000-37853400	Weak transcription	Stomach Mucosa	stomach
11	chr19:37828000-37855800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:37830000-37846800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:37830000-37853600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:37830800-37853200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:37831800-37846400	Strong transcription	Dnd41	blood
16	chr19:37832600-37852200	Weak transcription	Fetal Thymus	thymus
17	chr19:37832800-37850800	Weak transcription	HMEC	breast
18	chr19:37832800-37852400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:37833000-37845400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:37834400-37845200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:37834400-37847800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr19:37834600-37845600	Strong transcription	Primary B cells from cord blood	blood
23	chr19:37834600-37846000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:37834600-37846800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:37834800-37846000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr19:37836000-37845400	Weak transcription	Fetal Kidney	kidney
27	chr19:37836800-37852000	Weak transcription	Aorta	Aorta
28	chr19:37837000-37846400	Weak transcription	NHDF-Ad	bronchial
29	chr19:37837200-37847000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr19:37837800-37852200	Weak transcription	Right Ventricle	heart
31	chr19:37838800-37846800	Weak transcription	Colon Smooth Muscle	Colon
32	chr19:37839000-37847800	Weak transcription	Fetal Muscle Leg	muscle
33	chr19:37839000-37850000	Weak transcription	Spleen	Spleen
34	chr19:37839000-37850400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:37839000-37852800	Weak transcription	Brain Substantia Nigra	brain
36	chr19:37839200-37850200	Weak transcription	HepG2	liver
37	chr19:37839200-37851400	Weak transcription	HUVEC	blood vessel
38	chr19:37839600-37853200	Weak transcription	Hela-S3	cervix
39	chr19:37839800-37853600	Weak transcription	Fetal Heart	heart
40	chr19:37840000-37844800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr19:37840000-37845400	Weak transcription	Brain Germinal Matrix	brain
42	chr19:37840000-37845600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:37840000-37846200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:37840000-37846800	Weak transcription	Fetal Brain Male	brain
45	chr19:37840000-37846800	Weak transcription	Psoas Muscle	Psoas
46	chr19:37840200-37845600	Weak transcription	Brain Anterior Caudate	brain
47	chr19:37840200-37845800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:37840200-37846400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr19:37840200-37846800	Weak transcription	Colonic Mucosa	Colon
50	chr19:37840200-37848000	Weak transcription	Osteobl	bone

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