Variant report

Variant	rs2682588
Chromosome Location	chr19:44087726-44087727
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44080117..44083864-chr19:44085399..44088767,4	K562	blood:

Variant related genes	Relation type
ENSG00000073050	Chromatin interaction
ENSG00000234465	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11407	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes]
rs2021092	0.83[EUR][1000 genomes]
rs2307187	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs25484	0.80[EUR][1000 genomes]
rs2599464	0.80[EUR][1000 genomes]
rs2682552	0.80[CEU][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs2682560	0.80[EUR][1000 genomes]
rs2682562	0.80[EUR][1000 genomes]
rs2682587	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes]
rs2854495	0.89[EUR][1000 genomes]
rs2854496	0.80[CEU][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs2854497	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2854498	0.89[EUR][1000 genomes]
rs2854502	0.80[EUR][1000 genomes]
rs2854505	0.85[EUR][1000 genomes]
rs2854510	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304729	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs304730	0.85[EUR][1000 genomes]
rs3213251	1.00[ASN][1000 genomes]
rs3213283	0.84[EUR][1000 genomes]
rs3213285	0.82[EUR][1000 genomes]
rs3213289	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213293	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3213321	1.00[CHB][hapmap]
rs3213322	1.00[CHB][hapmap]
rs346049	1.00[CHB][hapmap]
rs73556510	1.00[ASN][1000 genomes]
rs73556512	1.00[ASN][1000 genomes]
rs73556542	1.00[ASN][1000 genomes]
rs8104645	1.00[CHB][hapmap]
rs939460	0.80[CEU][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2682588	PHLDB3	cis	lesional skin	skin_eQTL
rs2682588	PHLDB3	cis	normal skin	skin_eQTL
rs2682588	ZNF575	cis	Adipose Subcutaneous	GTEx
rs2682588	LOC390940	cis	uninvolved skin	skin_eQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44079800-44098200	Weak transcription	Small Intestine	intestine
2	chr19:44080400-44090200	Weak transcription	HSMM	muscle
3	chr19:44080600-44090800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:44080600-44095600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:44080800-44088400	Weak transcription	A549	lung
6	chr19:44081400-44090200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:44081400-44090200	Weak transcription	NHEK	skin
8	chr19:44081600-44090600	Weak transcription	HMEC	breast
9	chr19:44083000-44087800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:44084600-44088200	Weak transcription	Liver	Liver
11	chr19:44084600-44088400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr19:44084600-44090200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:44084600-44090200	Enhancers	Primary B cells from cord blood	blood
14	chr19:44084600-44090200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:44084600-44090400	Enhancers	Primary B cells from peripheral blood	blood
16	chr19:44084600-44093000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:44084600-44093000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:44084600-44093000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:44084600-44093000	Weak transcription	HUVEC	blood vessel
20	chr19:44084600-44093800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:44084600-44094000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:44084600-44096800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr19:44084600-44098200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:44084800-44089800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:44084800-44095400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr19:44084800-44097400	Weak transcription	NH-A	brain
27	chr19:44085000-44089800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:44085000-44095600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:44085000-44095600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:44085400-44094600	Weak transcription	Left Ventricle	heart
31	chr19:44085600-44088400	Weak transcription	Pancreas	Pancrea
32	chr19:44085600-44090000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:44085600-44090000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr19:44085600-44090200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:44085600-44090600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:44085600-44090600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:44085600-44094200	Weak transcription	Right Ventricle	heart
38	chr19:44085600-44095200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr19:44085600-44096200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:44085600-44096200	Weak transcription	Aorta	Aorta
41	chr19:44085600-44098800	Weak transcription	Psoas Muscle	Psoas
42	chr19:44085600-44099000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr19:44085800-44088000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:44085800-44088200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr19:44085800-44089000	Weak transcription	Fetal Intestine Large	intestine
46	chr19:44085800-44089800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:44085800-44090000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr19:44085800-44090000	Weak transcription	Osteobl	bone
49	chr19:44085800-44090200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr19:44085800-44090200	Weak transcription	Lung	lung

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