Variant report

Variant	rs13117918
Chromosome Location	chr4:7815739-7815740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11721583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11721609	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11724632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729332	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11729602	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11730169	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11731942	0.86[CEU][hapmap];0.82[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11733311	0.84[EUR][1000 genomes]
rs11734524	0.87[EUR][1000 genomes]
rs11734860	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11736215	0.88[CHB][hapmap]
rs11737447	0.89[CEU][hapmap];0.88[CHB][hapmap];0.85[EUR][1000 genomes]
rs13113113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13121514	1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs13125295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13128495	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs13132939	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17382379	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs17382393	0.86[EUR][1000 genomes]
rs17466895	0.86[EUR][1000 genomes]
rs34250310	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34352176	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34949259	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35041036	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35161247	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35281689	0.84[AFR][1000 genomes]
rs35509185	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35515779	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35592594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35617438	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35672467	0.91[AFR][1000 genomes]
rs35870249	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35889107	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3934645	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41264705	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4443284	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4594724	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55698135	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55740648	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56270003	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56352084	0.84[EUR][1000 genomes]
rs58457272	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61036795	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62289276	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62291980	0.86[EUR][1000 genomes]
rs62291982	0.84[AFR][1000 genomes]
rs62291983	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62291984	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs885260	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13117918	AFAP1	cis	cerebellum	SCAN
rs13117918	CLNK	cis	cerebellum	SCAN
rs13117918	AFAP	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
3	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr4:7800600-7828800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:7802200-7819800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:7804000-7829200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:7805200-7822600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:7805600-7816400	Genic enhancers	Fetal Stomach	stomach
10	chr4:7806200-7819200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:7806400-7824600	Weak transcription	Fetal Thymus	thymus
12	chr4:7807800-7817800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:7808000-7823000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:7808600-7830000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:7808800-7818400	Weak transcription	Psoas Muscle	Psoas
16	chr4:7809200-7816600	Weak transcription	Fetal Brain Male	brain
17	chr4:7809600-7819000	Genic enhancers	A549	lung
18	chr4:7809600-7822400	Weak transcription	Brain Substantia Nigra	brain
19	chr4:7809600-7823000	Weak transcription	Brain Angular Gyrus	brain
20	chr4:7809600-7828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:7809800-7820000	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:7809800-7823400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:7809800-7823400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:7810000-7816200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:7810000-7816200	Weak transcription	Aorta	Aorta
26	chr4:7810000-7823400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:7810200-7821000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:7810600-7816200	Weak transcription	Left Ventricle	heart
29	chr4:7810800-7816200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr4:7811200-7817400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:7811400-7816000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:7811400-7819600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:7811600-7816400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr4:7811800-7816200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:7812200-7816400	Enhancers	Fetal Heart	heart
36	chr4:7812800-7816000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr4:7812800-7822200	Genic enhancers	NH-A	brain
38	chr4:7813200-7816200	Weak transcription	Fetal Brain Female	brain
39	chr4:7813400-7816200	Weak transcription	Lung	lung
40	chr4:7813400-7819800	Weak transcription	Right Atrium	heart
41	chr4:7813400-7825200	Weak transcription	Right Ventricle	heart
42	chr4:7813400-7829800	Weak transcription	Spleen	Spleen
43	chr4:7814000-7816000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:7814000-7816000	Weak transcription	Gastric	stomach
45	chr4:7814000-7816200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:7814000-7816200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr4:7814000-7816400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr4:7814000-7817600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:7814000-7818600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr4:7814000-7819800	Weak transcription	Colonic Mucosa	Colon

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