Variant report

Variant	rs1048518
Chromosome Location	chr4:106392707-106392708
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:106061821..106062508-chr4:106392423..106393188,2	K562	blood:
2	chr4:106066483..106069673-chr4:106390838..106393733,3	K562	blood:
3	chr4:106060523..106062575-chr4:106390965..106392720,2	K562	blood:
4	chr4:106391240..106392982-chr4:106630165..106631896,2	K562	blood:
5	chr4:106270792..106273529-chr4:106390596..106392898,2	K562	blood:
6	chr4:105848795..105851289-chr4:106392054..106394222,2	MCF-7	breast:
7	chr4:106066539..106069010-chr4:106392150..106395317,5	MCF-7	breast:
8	chr4:106373864..106376614-chr4:106391989..106394662,2	MCF-7	breast:
9	chr4:106046108..106050165-chr4:106391446..106394724,4	MCF-7	breast:
10	chr4:106060470..106063103-chr4:106391322..106393340,2	K562	blood:
11	chr4:106064984..106068563-chr4:106391196..106395238,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction
ENSG00000251259	Chromatin interaction
ENSG00000138785	Chromatin interaction
ENSG00000138777	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12498981	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12507480	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12644313	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17008180	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28723530	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7660502	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002228	chr4:106346206-106433381	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1048518	PPA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106347600-106392800	Weak transcription	Colonic Mucosa	Colon
2	chr4:106348200-106393000	Weak transcription	Thymus	Thymus
3	chr4:106355400-106393200	Weak transcription	Esophagus	oesophagus
4	chr4:106366800-106393200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:106374000-106393000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:106375400-106393000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:106375400-106393000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:106377000-106393000	Weak transcription	Right Atrium	heart
9	chr4:106377000-106393200	Weak transcription	Pancreas	Pancrea
10	chr4:106377000-106394000	Weak transcription	Gastric	stomach
11	chr4:106378000-106393000	Weak transcription	HSMMtube	muscle
12	chr4:106381200-106394000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:106382800-106392800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:106383400-106393000	Weak transcription	Fetal Brain Female	brain
15	chr4:106385000-106394000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:106385200-106393400	Weak transcription	Brain Germinal Matrix	brain
17	chr4:106386400-106394200	Weak transcription	Spleen	Spleen
18	chr4:106388200-106392800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:106388200-106392800	Weak transcription	Fetal Thymus	thymus
20	chr4:106388400-106393000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:106388400-106393200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:106388400-106393200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:106388400-106394000	Weak transcription	Lung	lung
24	chr4:106388600-106392800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:106388600-106392800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:106388600-106392800	Weak transcription	Fetal Intestine Large	intestine
27	chr4:106388600-106394000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:106389000-106393200	Weak transcription	Placenta	Placenta
29	chr4:106389400-106392800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr4:106389400-106393000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:106389800-106392800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr4:106389800-106393000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:106390200-106392800	Weak transcription	Ovary	ovary
34	chr4:106390600-106393000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:106390800-106393000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:106391200-106393600	Enhancers	Primary B cells from cord blood	blood
37	chr4:106391400-106392800	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr4:106391800-106392800	Enhancers	Primary T cells from cord blood	blood
39	chr4:106392000-106392800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:106392000-106392800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
41	chr4:106392000-106393000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr4:106392200-106392800	Enhancers	Fetal Intestine Small	intestine
43	chr4:106392200-106393000	Enhancers	Colon Smooth Muscle	Colon
44	chr4:106392200-106393200	Enhancers	Primary hematopoietic stem cells	blood
45	chr4:106392200-106394200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr4:106392200-106394600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:106392400-106392800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:106392400-106392800	Enhancers	Brain Substantia Nigra	brain
49	chr4:106392400-106392800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr4:106392400-106392800	Enhancers	Hela-S3	cervix

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