Variant report

Variant	rs2636693
Chromosome Location	chr4:106294756-106294757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10020998	0.82[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.88[TSI][hapmap]
rs10024331	0.82[CEU][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs1125254	0.82[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs11301777	0.98[ASN][1000 genomes]
rs1603706	0.97[ASN][1000 genomes]
rs2023840	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2046880	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2264415	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2264416	0.97[ASN][1000 genomes]
rs2264853	0.97[ASN][1000 genomes]
rs2298732	0.87[CHB][hapmap];0.90[CHD][hapmap];0.82[MEX][hapmap]
rs2636694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2636695	0.97[ASN][1000 genomes]
rs2636727	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2636747	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2647242	0.95[ASN][1000 genomes]
rs2647252	0.97[ASN][1000 genomes]
rs2647255	0.96[ASN][1000 genomes]
rs2647265	0.93[ASN][1000 genomes]
rs2713826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2713844	0.97[ASN][1000 genomes]
rs2713845	0.97[ASN][1000 genomes]
rs2726456	0.98[ASN][1000 genomes]
rs2726496	0.97[ASN][1000 genomes]
rs2866883	0.87[CHB][hapmap]
rs34248474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35206705	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36112402	0.98[ASN][1000 genomes]
rs3864225	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs4235414	0.82[CEU][hapmap]
rs4699176	0.82[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs6533199	0.82[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs6533201	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs6816997	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs72665982	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs763289	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs7678401	0.87[CHB][hapmap];0.90[CHD][hapmap];0.82[MEX][hapmap]
rs924282	0.96[ASN][1000 genomes]
rs924283	0.96[ASN][1000 genomes]
rs9999896	0.82[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]

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	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
7	nsv980463	chr4:106294684-106304254	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2636693	PPA2	cis	Lymphoblastoid	GTEx
rs2636693	PPA2	cis	multi-tissue	Pritchard
rs2636693	PPA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:106 , 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	chr4:106272800-106304000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:106274400-106326800	Weak transcription	Small Intestine	intestine
4	chr4:106274800-106330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr4:106275800-106307800	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:106278600-106307600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:106279000-106339600	Weak transcription	HSMMtube	muscle
8	chr4:106279000-106347400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:106280000-106344600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:106281000-106326800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:106282600-106316800	Weak transcription	Fetal Heart	heart
12	chr4:106282600-106325800	Weak transcription	Brain Angular Gyrus	brain
13	chr4:106282600-106335600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:106283600-106330000	Weak transcription	Right Ventricle	heart
15	chr4:106285000-106326000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:106286600-106295400	Weak transcription	Hela-S3	cervix
17	chr4:106287000-106320800	Weak transcription	NH-A	brain
18	chr4:106287000-106335800	Weak transcription	Colonic Mucosa	Colon
19	chr4:106287600-106304000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:106287600-106304800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:106287600-106335600	Weak transcription	Esophagus	oesophagus
22	chr4:106287600-106357000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:106287800-106303800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:106287800-106303800	Weak transcription	Fetal Stomach	stomach
25	chr4:106287800-106304000	Weak transcription	Ovary	ovary
26	chr4:106287800-106306000	Weak transcription	Placenta	Placenta
27	chr4:106287800-106318600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:106287800-106320000	Weak transcription	A549	lung
29	chr4:106287800-106326800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:106287800-106330200	Weak transcription	Gastric	stomach
31	chr4:106287800-106335400	Weak transcription	Spleen	Spleen
32	chr4:106287800-106335800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:106287800-106347600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:106288400-106297200	Weak transcription	HMEC	breast
35	chr4:106288400-106306000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:106288400-106318600	Weak transcription	Aorta	Aorta
37	chr4:106288400-106330200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:106288400-106330200	Weak transcription	Lung	lung
39	chr4:106288600-106304000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr4:106288600-106325600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr4:106288600-106335400	Weak transcription	Thymus	Thymus
42	chr4:106288800-106303800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:106288800-106320600	Weak transcription	NHEK	skin
44	chr4:106288800-106325600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr4:106289200-106325600	Weak transcription	Fetal Muscle Leg	muscle
46	chr4:106289400-106316800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:106289600-106335400	Weak transcription	Brain Anterior Caudate	brain
48	chr4:106290000-106306000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:106290000-106347400	Weak transcription	Fetal Kidney	kidney
50	chr4:106290200-106295400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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