Variant report

Variant	rs3898404
Chromosome Location	chr4:106356395-106356396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106354505..106356788-chr4:106358745..106361316,2	K562	blood:
2	chr4:106355071..106357456-chr4:106372539..106374693,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1017988	1.00[ASN][1000 genomes]
rs1077526	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1126066	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035461	0.82[EUR][1000 genomes]
rs17035475	1.00[CHD][hapmap]
rs17035550	1.00[CEU][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035551	1.00[CEU][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035553	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035557	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035558	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035568	1.00[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035581	1.00[ASN][1000 genomes]
rs17035584	1.00[ASN][1000 genomes]
rs17035586	1.00[ASN][1000 genomes]
rs17035619	1.00[ASN][1000 genomes]
rs17509136	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1874758	0.82[CEU][hapmap]
rs2004290	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41438151	1.00[CHD][hapmap];0.89[MEX][hapmap]
rs4499701	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519798	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55652556	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55755102	1.00[ASN][1000 genomes]
rs55874621	1.00[ASN][1000 genomes]
rs56397029	1.00[ASN][1000 genomes]
rs59902936	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62317353	1.00[ASN][1000 genomes]
rs6533194	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]
rs66517713	1.00[ASN][1000 genomes]
rs66763438	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66932244	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66956902	1.00[ASN][1000 genomes]
rs66988826	1.00[ASN][1000 genomes]
rs67248885	1.00[ASN][1000 genomes]
rs67476913	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67554145	1.00[ASN][1000 genomes]
rs6811159	1.00[ASN][1000 genomes]
rs6829168	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856615	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857688	0.82[EUR][1000 genomes]
rs72668208	1.00[ASN][1000 genomes]
rs72668215	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668219	1.00[ASN][1000 genomes]
rs72668239	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3898404	PPA2	cis	multi-tissue	Pritchard
rs3898404	PPA2	cis	brain	seeQTL
rs3898404	PPA2	Cis_1M	lymphoblastoid	RTeQTL
rs3898404	BANK1	cis	parietal	SCAN
rs3898404	SGMS2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106287600-106357000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr4:106321400-106367200	Weak transcription	HUVEC	blood vessel
3	chr4:106323600-106372800	Weak transcription	Stomach Mucosa	stomach
4	chr4:106326000-106356400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:106326000-106356600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:106326000-106363200	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:106327200-106365200	Weak transcription	Osteobl	bone
8	chr4:106327200-106389200	Weak transcription	Small Intestine	intestine
9	chr4:106327200-106390600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:106330600-106356400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:106336600-106356400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:106336800-106376400	Weak transcription	Right Ventricle	heart
13	chr4:106336800-106387800	Weak transcription	NHLF	lung
14	chr4:106337200-106356600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:106340200-106387800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:106341600-106376000	Weak transcription	Fetal Heart	heart
17	chr4:106343200-106363000	Weak transcription	Psoas Muscle	Psoas
18	chr4:106344000-106363800	Weak transcription	HepG2	liver
19	chr4:106345200-106358800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:106346600-106369000	Weak transcription	Hela-S3	cervix
21	chr4:106347200-106366000	Weak transcription	NHDF-Ad	bronchial
22	chr4:106347600-106367600	Weak transcription	Fetal Brain Male	brain
23	chr4:106347600-106392800	Weak transcription	Colonic Mucosa	Colon
24	chr4:106347800-106357200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:106347800-106362800	Weak transcription	Spleen	Spleen
26	chr4:106347800-106375200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr4:106348000-106356400	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:106348000-106356600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:106348000-106366000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:106348000-106375000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:106348000-106376400	Weak transcription	Gastric	stomach
32	chr4:106348000-106376800	Weak transcription	Pancreas	Pancrea
33	chr4:106348000-106388000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:106348200-106356400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr4:106348200-106356600	Weak transcription	Brain Substantia Nigra	brain
36	chr4:106348200-106363800	Weak transcription	Aorta	Aorta
37	chr4:106348200-106364400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:106348200-106387800	Weak transcription	Lung	lung
39	chr4:106348200-106393000	Weak transcription	Thymus	Thymus
40	chr4:106348400-106384200	Weak transcription	Fetal Stomach	stomach
41	chr4:106348600-106356400	Weak transcription	Fetal Kidney	kidney
42	chr4:106348600-106384600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:106348800-106356600	Weak transcription	Brain Anterior Caudate	brain
44	chr4:106348800-106357000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr4:106348800-106375000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr4:106349200-106356600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:106349600-106356600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr4:106349800-106360200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr4:106350200-106356600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr4:106351400-106356600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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