Variant report

Variant	rs13119659
Chromosome Location	chr4:76720885-76720886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10009902	0.81[ASN][1000 genomes]
rs10014281	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10028291	0.88[TSI][hapmap]
rs10028884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10031532	0.88[YRI][hapmap]
rs10212995	0.93[TSI][hapmap]
rs11097070	0.82[CHB][hapmap]
rs11729258	0.82[CHB][hapmap]
rs11736474	0.82[CHB][hapmap]
rs11938067	0.93[TSI][hapmap]
rs13110602	0.93[TSI][hapmap]
rs13145290	0.93[TSI][hapmap]
rs1553984	1.00[JPT][hapmap]
rs1967495	0.82[CHB][hapmap]
rs1967496	0.82[CHB][hapmap]
rs226416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2280095	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324682	0.93[ASN][1000 genomes]
rs324683	0.93[ASN][1000 genomes]
rs324685	0.93[ASN][1000 genomes]
rs324687	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs324689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs324692	0.93[ASN][1000 genomes]
rs324694	0.93[ASW][hapmap];0.97[LWK][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes]
rs324695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs324702	0.94[AFR][1000 genomes]
rs324704	0.87[YRI][hapmap]
rs324707	0.88[ASN][1000 genomes]
rs324708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs324710	0.86[YRI][hapmap]
rs324711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs324715	0.88[ASN][1000 genomes]
rs324716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs324717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs324718	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs324721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs324724	0.93[ASN][1000 genomes]
rs324725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs324729	0.94[AFR][1000 genomes]
rs324734	0.81[LWK][hapmap];0.88[YRI][hapmap]
rs324737	0.93[ASN][1000 genomes]
rs3796473	0.82[CHB][hapmap]
rs3853183	0.82[CHB][hapmap]
rs3853184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs436611	0.88[ASN][1000 genomes]
rs443952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4859406	0.93[TSI][hapmap]
rs4859408	0.93[TSI][hapmap]
rs4859543	0.82[CHB][hapmap]
rs4859548	0.82[CHB][hapmap]
rs4859550	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4859552	0.93[TSI][hapmap]
rs5020591	0.83[ASN][1000 genomes]
rs6419115	0.88[ASN][1000 genomes]
rs6531889	1.00[JPT][hapmap]
rs6531902	0.83[ASN][1000 genomes]
rs6531903	0.83[ASN][1000 genomes]
rs6826858	0.82[CHB][hapmap]
rs6827809	1.00[CHB][hapmap]
rs6835819	0.83[ASN][1000 genomes]
rs6842216	0.83[ASN][1000 genomes]
rs6843016	0.93[TSI][hapmap]
rs6847333	0.93[TSI][hapmap]
rs6855321	0.83[ASN][1000 genomes]
rs72651313	0.93[ASN][1000 genomes]
rs7655464	0.91[TSI][hapmap]
rs7662940	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7677150	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7691385	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1003516	chr4:76597112-76729576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv537143	chr4:76597112-76729576	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13119659	PPEF2	cis	parietal	SCAN
rs13119659	FAM47E	cis	parietal	SCAN
rs13119659	USO1	cis	cerebellum	SCAN
rs13119659	CCNG2	cis	cerebellum	SCAN
rs13119659	CDKL2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76650800-76737800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:76652400-76725000	Weak transcription	Hela-S3	cervix
3	chr4:76671000-76739400	Weak transcription	Stomach Mucosa	stomach
4	chr4:76675000-76727400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:76676400-76730600	Weak transcription	Spleen	Spleen
6	chr4:76677000-76736200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:76685800-76738400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr4:76688200-76738200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:76689400-76724000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:76697600-76734400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:76698000-76721600	Weak transcription	Brain Anterior Caudate	brain
12	chr4:76698000-76735400	Weak transcription	Small Intestine	intestine
13	chr4:76698800-76725000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:76699000-76725400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:76699200-76724000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:76699400-76722600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:76701200-76725200	Weak transcription	Thymus	Thymus
18	chr4:76701800-76721800	Weak transcription	Colonic Mucosa	Colon
19	chr4:76703400-76722800	Weak transcription	Psoas Muscle	Psoas
20	chr4:76704200-76722400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:76704800-76725200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:76705000-76730800	Weak transcription	Fetal Heart	heart
23	chr4:76705800-76721400	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:76705800-76725200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:76705800-76730600	Weak transcription	Fetal Brain Female	brain
26	chr4:76706000-76722800	Weak transcription	Ovary	ovary
27	chr4:76706000-76730600	Weak transcription	Aorta	Aorta
28	chr4:76706000-76732000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:76706000-76732000	Weak transcription	Gastric	stomach
30	chr4:76706200-76725000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:76707800-76738600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:76708400-76721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:76708400-76725200	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:76708400-76735400	Weak transcription	Right Ventricle	heart
35	chr4:76710600-76721400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:76710800-76729400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:76711800-76721600	Weak transcription	Fetal Kidney	kidney
38	chr4:76711800-76729400	Weak transcription	Fetal Brain Male	brain
39	chr4:76711800-76729400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr4:76712000-76722400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr4:76712200-76721400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr4:76712200-76729600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr4:76712200-76730600	Weak transcription	Brain Angular Gyrus	brain
44	chr4:76712400-76721400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:76712400-76721400	Weak transcription	K562	blood
46	chr4:76712400-76721600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:76712400-76722000	Weak transcription	Brain Substantia Nigra	brain
48	chr4:76712400-76725000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:76712400-76729200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:76712600-76730600	Weak transcription	Brain Germinal Matrix	brain

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