Variant report

Variant	rs13123933
Chromosome Location	chr4:106288192-106288193
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	chr4:106288031..106290693-chr4:106292188..106294028,2	K562	blood:
2	chr4:106287631..106290693-chr4:106292188..106294028,3	K562	blood:

Extended variants
information (count: 130 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10015293	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11733020	0.82[ASN][1000 genomes]
rs12643660	0.89[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.89[ASN][1000 genomes]
rs13134204	0.81[ASN][1000 genomes]
rs13787	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs1490590	0.81[ASN][1000 genomes]
rs1490591	0.96[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1490592	0.81[ASN][1000 genomes]
rs1490593	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1490594	0.80[ASN][1000 genomes]
rs1490595	0.80[JPT][hapmap]
rs1490603	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1490604	0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1490605	0.81[ASN][1000 genomes]
rs1490606	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1490607	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1490608	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1565484	0.81[ASN][1000 genomes]
rs1565485	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17321073	0.82[EUR][1000 genomes]
rs1844656	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1994636	0.80[JPT][hapmap]
rs1994637	0.81[JPT][hapmap]
rs2077608	1.00[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2130693	0.88[EUR][1000 genomes]
rs2130694	0.96[CEU][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2172028	0.81[ASN][1000 genomes]
rs2466916	0.86[EUR][1000 genomes]
rs2522545	0.80[JPT][hapmap]
rs2636696	0.80[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636698	0.80[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636700	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2636701	0.81[ASN][1000 genomes]
rs2636703	0.81[ASN][1000 genomes]
rs2636704	0.81[ASN][1000 genomes]
rs2636706	0.81[ASN][1000 genomes]
rs2636707	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2636708	0.81[JPT][hapmap]
rs2636709	0.81[ASN][1000 genomes]
rs2636713	0.80[JPT][hapmap]
rs2636718	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2636721	0.80[ASN][1000 genomes]
rs2636722	0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2636723	0.81[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2636725	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2636726	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2636728	0.81[ASN][1000 genomes]
rs2636729	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2636730	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2636731	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2636732	1.00[CEU][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes]
rs2636733	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2636734	0.95[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs2636735	0.81[JPT][hapmap]
rs2636739	0.80[JPT][hapmap]
rs2636741	0.96[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs2636742	0.95[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2636743	1.00[CEU][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes]
rs2636746	0.81[JPT][hapmap]
rs2636749	0.81[JPT][hapmap]
rs2636751	0.80[JPT][hapmap]
rs2647254	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2713822	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2713827	0.88[CEU][hapmap];0.80[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2713829	0.80[JPT][hapmap]
rs2713830	0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2713831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2713832	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2713833	0.81[CEU][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2713834	1.00[CEU][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2713835	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2713836	0.81[ASN][1000 genomes]
rs2713838	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs2713841	0.81[JPT][hapmap]
rs2713842	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2713843	0.81[ASN][1000 genomes]
rs2713847	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2713850	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2713852	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2713853	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2713854	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2713859	0.81[JPT][hapmap]
rs2713860	0.96[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2713861	0.80[JPT][hapmap]
rs2713863	0.96[CEU][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes]
rs2713866	0.81[ASN][1000 genomes]
rs2713867	0.81[ASN][1000 genomes]
rs2713868	0.81[ASN][1000 genomes]
rs2713869	0.81[ASN][1000 genomes]
rs2713870	0.81[ASN][1000 genomes]
rs2713871	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2713873	0.96[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2713874	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2713875	0.89[EUR][1000 genomes]
rs2713876	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2726453	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2726454	0.96[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2726455	1.00[CEU][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2726462	0.83[JPT][hapmap]
rs2726463	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2726468	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2726494	0.81[ASN][1000 genomes]
rs2726495	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2726497	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2726499	0.81[JPT][hapmap]
rs2726502	0.80[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2726503	0.82[ASN][1000 genomes]
rs2726506	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2726511	0.92[ASN][1000 genomes]
rs2726514	0.87[EUR][1000 genomes]
rs2726515	0.81[JPT][hapmap]
rs2726516	0.80[JPT][hapmap]
rs2726526	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2866884	0.81[JPT][hapmap]
rs4450931	0.80[JPT][hapmap]
rs4467572	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61117510	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs716205	0.81[ASN][1000 genomes]
rs753972	0.92[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7673368	0.80[JPT][hapmap]
rs923587	0.80[JPT][hapmap]
rs923589	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs923590	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9992793	0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv879698	chr4:106155751-106309224	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13123933	PPA2	cis	Lymphoblastoid	GTEx
rs13123933	PPA2	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106253800-106343000	Weak transcription	Psoas Muscle	Psoas
2	chr4:106272600-106291600	Weak transcription	Fetal Brain Male	brain
3	chr4:106272800-106304000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:106273400-106288200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:106273400-106293000	Weak transcription	Pancreas	Pancrea
6	chr4:106274200-106288200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:106274400-106326800	Weak transcription	Small Intestine	intestine
8	chr4:106274800-106294400	Weak transcription	HSMM	muscle
9	chr4:106274800-106330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr4:106275800-106307800	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:106277600-106288200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:106278600-106307600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:106279000-106339600	Weak transcription	HSMMtube	muscle
14	chr4:106279000-106347400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:106279600-106288600	Weak transcription	Fetal Kidney	kidney
16	chr4:106279800-106288400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr4:106280000-106344600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:106280600-106290600	Weak transcription	Stomach Mucosa	stomach
19	chr4:106280800-106288600	Weak transcription	Adipose Nuclei	Adipose
20	chr4:106281000-106326800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:106281400-106288800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:106282400-106289000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:106282600-106316800	Weak transcription	Fetal Heart	heart
24	chr4:106282600-106325800	Weak transcription	Brain Angular Gyrus	brain
25	chr4:106282600-106335600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:106282800-106288200	Weak transcription	Brain Substantia Nigra	brain
27	chr4:106283200-106290800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:106283600-106330000	Weak transcription	Right Ventricle	heart
29	chr4:106285000-106289200	Weak transcription	Osteobl	bone
30	chr4:106285000-106326000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:106285600-106288400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
32	chr4:106285600-106288400	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr4:106285600-106289000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:106286000-106288400	Strong transcription	Aorta	Aorta
35	chr4:106286200-106288400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:106286400-106288600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:106286600-106288600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
38	chr4:106286600-106295400	Weak transcription	Hela-S3	cervix
39	chr4:106286800-106288800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
40	chr4:106286800-106291000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:106287000-106288400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr4:106287000-106288400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr4:106287000-106288600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:106287000-106288600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:106287000-106288600	ZNF genes & repeats	Thymus	Thymus
46	chr4:106287000-106288800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:106287000-106289000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:106287000-106290800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:106287000-106291200	Strong transcription	Primary T cells from cord blood	blood
50	chr4:106287000-106291400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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