Variant report

Variant	rs6533194
Chromosome Location	chr4:106363619-106363620
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106361657..106363755-chr4:106371118..106372722,2	K562	blood:
2	chr4:106361557..106363755-chr4:106371122..106372722,2	K562	blood:
3	chr4:106362358..106365940-chr4:106392957..106394904,3	MCF-7	breast:
4	chr4:106362935..106364734-chr4:106393574..106395649,2	K562	blood:

Variant related genes	Relation type
ENSG00000138777	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1017988	1.00[ASN][1000 genomes]
rs1077526	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126066	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035461	0.83[EUR][1000 genomes]
rs17035550	1.00[CEU][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035551	1.00[CEU][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035553	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035557	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035558	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035568	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035581	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035584	1.00[ASN][1000 genomes]
rs17035586	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17035619	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509136	1.00[ASN][1000 genomes]
rs1874758	0.80[CEU][hapmap]
rs2004290	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898404	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4499701	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519798	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55652556	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55755102	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55874621	1.00[ASN][1000 genomes]
rs56397029	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59902936	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317353	1.00[ASN][1000 genomes]
rs66517713	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66763438	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66932244	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66956902	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66988826	1.00[ASN][1000 genomes]
rs67248885	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67476913	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67554145	1.00[ASN][1000 genomes]
rs6811159	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829168	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856615	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857688	0.84[EUR][1000 genomes]
rs72668208	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668215	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668219	1.00[ASN][1000 genomes]
rs72668239	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	esv2760858	chr4:106351454-106376197	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6533194	PPA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106321400-106367200	Weak transcription	HUVEC	blood vessel
2	chr4:106323600-106372800	Weak transcription	Stomach Mucosa	stomach
3	chr4:106327200-106365200	Weak transcription	Osteobl	bone
4	chr4:106327200-106389200	Weak transcription	Small Intestine	intestine
5	chr4:106327200-106390600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:106336800-106376400	Weak transcription	Right Ventricle	heart
7	chr4:106336800-106387800	Weak transcription	NHLF	lung
8	chr4:106340200-106387800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:106341600-106376000	Weak transcription	Fetal Heart	heart
10	chr4:106344000-106363800	Weak transcription	HepG2	liver
11	chr4:106346600-106369000	Weak transcription	Hela-S3	cervix
12	chr4:106347200-106366000	Weak transcription	NHDF-Ad	bronchial
13	chr4:106347600-106367600	Weak transcription	Fetal Brain Male	brain
14	chr4:106347600-106392800	Weak transcription	Colonic Mucosa	Colon
15	chr4:106347800-106375200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr4:106348000-106366000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:106348000-106375000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:106348000-106376400	Weak transcription	Gastric	stomach
19	chr4:106348000-106376800	Weak transcription	Pancreas	Pancrea
20	chr4:106348000-106388000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:106348200-106363800	Weak transcription	Aorta	Aorta
22	chr4:106348200-106364400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:106348200-106387800	Weak transcription	Lung	lung
24	chr4:106348200-106393000	Weak transcription	Thymus	Thymus
25	chr4:106348400-106384200	Weak transcription	Fetal Stomach	stomach
26	chr4:106348600-106384600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:106348800-106375000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:106352200-106375000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:106355400-106378800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:106355400-106393200	Weak transcription	Esophagus	oesophagus
31	chr4:106356800-106372600	Weak transcription	NH-A	brain
32	chr4:106357000-106372800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:106357200-106363800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:106357200-106364800	Weak transcription	NHEK	skin
35	chr4:106357200-106365200	Weak transcription	HSMM	muscle
36	chr4:106357200-106374200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:106357200-106381000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:106357200-106381000	Weak transcription	Brain Substantia Nigra	brain
39	chr4:106357200-106387600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:106357200-106392600	Weak transcription	Brain Angular Gyrus	brain
41	chr4:106357600-106363800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:106357600-106364200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:106357600-106392200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:106357800-106371400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:106358000-106369200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:106358200-106369600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:106358400-106367400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr4:106358600-106370200	Weak transcription	K562	blood
49	chr4:106358800-106372600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr4:106359000-106363800	Weak transcription	Brain Hippocampus Middle	brain

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