Variant report

Variant	rs4699177
Chromosome Location	chr4:106392086-106392087
allele	A/C
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:106066483..106069673-chr4:106390838..106393733,3	K562	blood:
2	chr4:106060523..106062575-chr4:106390965..106392720,2	K562	blood:
3	chr4:106065001..106068039-chr4:106390236..106392618,4	MCF-7	breast:
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	chr4:106373864..106376614-chr4:106391989..106394662,2	MCF-7	breast:
8	chr4:106046108..106050165-chr4:106391446..106394724,4	MCF-7	breast:
9	chr4:106060470..106063103-chr4:106391322..106393340,2	K562	blood:
10	chr4:106064984..106068563-chr4:106391196..106395238,6	K562	blood:

No data

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

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10050189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13104830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129703	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074396	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28706361	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28707313	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6817372	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4699177	PPA2	cis	Lymphoblastoid	GTEx
rs4699177	PPA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 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	chr4:106357200-106392600	Weak transcription	Brain Angular Gyrus	brain
5	chr4:106357600-106392200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:106362200-106392600	Weak transcription	A549	lung
7	chr4:106364600-106392600	Weak transcription	Fetal Kidney	kidney
8	chr4:106366000-106392400	Weak transcription	Osteobl	bone
9	chr4:106366000-106392600	Weak transcription	Psoas Muscle	Psoas
10	chr4:106366600-106392200	Weak transcription	Liver	Liver
11	chr4:106366600-106392200	Weak transcription	HepG2	liver
12	chr4:106366600-106392600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:106366800-106393200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:106370000-106392600	Weak transcription	HUVEC	blood vessel
15	chr4:106373200-106392600	Weak transcription	NH-A	brain
16	chr4:106373400-106392200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:106374000-106392400	Weak transcription	NHDF-Ad	bronchial
18	chr4:106374000-106393000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:106374600-106392400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:106374600-106392600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:106375400-106392600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:106375400-106393000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:106375400-106393000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:106376800-106392600	Weak transcription	Fetal Lung	lung
25	chr4:106377000-106393000	Weak transcription	Right Atrium	heart
26	chr4:106377000-106393200	Weak transcription	Pancreas	Pancrea
27	chr4:106377000-106394000	Weak transcription	Gastric	stomach
28	chr4:106378000-106392200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:106378000-106392200	Weak transcription	HMEC	breast
30	chr4:106378000-106392400	Weak transcription	HSMM	muscle
31	chr4:106378000-106393000	Weak transcription	HSMMtube	muscle
32	chr4:106379200-106392200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:106379200-106392600	Weak transcription	Aorta	Aorta
34	chr4:106379600-106392200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:106381200-106394000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:106381600-106392600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:106382000-106392400	Weak transcription	Brain Substantia Nigra	brain
38	chr4:106382800-106392600	Weak transcription	Stomach Mucosa	stomach
39	chr4:106382800-106392800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:106383200-106392400	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:106383400-106392400	Weak transcription	Fetal Heart	heart
42	chr4:106383400-106393000	Weak transcription	Fetal Brain Female	brain
43	chr4:106385000-106394000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:106385200-106393400	Weak transcription	Brain Germinal Matrix	brain
45	chr4:106385400-106392400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:106386400-106394200	Weak transcription	Spleen	Spleen
47	chr4:106386600-106392600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr4:106388200-106392400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:106388200-106392400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr4:106388200-106392400	Weak transcription	Rectal Mucosa Donor 29	rectum

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