Variant report

Variant	rs336298
Chromosome Location	chr4:143015352-143015353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10014809	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1039936	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461275	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10461276	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12501744	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12509457	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13327961	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs168061	0.80[JPT][hapmap]
rs17015503	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2292392	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2322307	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2322308	0.86[EUR][1000 genomes]
rs28413617	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28454477	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28460053	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28570218	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs336292	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336295	0.83[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs336296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336297	0.83[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs336300	0.83[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs336308	0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap]
rs336310	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs336312	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336318	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336319	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs336321	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336323	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336324	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336326	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336331	0.81[ASN][1000 genomes]
rs336332	0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs34087587	0.80[ASN][1000 genomes]
rs35981130	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3729592	0.84[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3756111	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3756112	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3756113	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3775621	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3775624	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3775625	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3775627	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3775628	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3775631	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3822135	0.84[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3822136	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3822137	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3822138	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3822139	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4388159	0.81[EUR][1000 genomes]
rs4637485	0.80[ASN][1000 genomes]
rs4989471	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6537099	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6537100	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6537101	0.84[CEU][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6826672	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6827563	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6853327	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6853350	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9996933	0.88[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830096	chr4:142867099-143023761	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv428775	chr4:142943213-143050195	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830097	chr4:142949705-143136372	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs336298	MAML3	cis	cerebellum	SCAN
rs336298	KRTAP22-1	trans	parietal	SCAN
rs336298	C4orf22	trans	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142948400-143029200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:142988000-143015400	Weak transcription	Aorta	Aorta
3	chr4:142988200-143029400	Weak transcription	Left Ventricle	heart
4	chr4:142990000-143051200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:142997800-143024600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:143001400-143040600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:143002600-143041800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:143004000-143015400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr4:143004000-143017000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:143004000-143021800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:143004600-143051600	Weak transcription	Pancreas	Pancrea
12	chr4:143006200-143016400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:143007200-143015400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:143007200-143016800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:143007400-143025400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:143007600-143024800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:143007800-143015400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:143008000-143025600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:143010400-143043400	Weak transcription	Psoas Muscle	Psoas
20	chr4:143010400-143057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:143011000-143015400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:143012400-143023000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr4:143012400-143040600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:143012800-143017400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:143013000-143016400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:143013000-143016400	Weak transcription	Osteobl	bone
27	chr4:143013000-143016600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:143013000-143016800	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:143013000-143017000	Weak transcription	NHLF	lung
30	chr4:143013200-143015800	Strong transcription	HSMMtube	muscle
31	chr4:143013400-143015400	Weak transcription	Esophagus	oesophagus
32	chr4:143013400-143015400	Enhancers	Hela-S3	cervix
33	chr4:143013400-143016800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:143013400-143017000	Weak transcription	Fetal Heart	heart
35	chr4:143013600-143016800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:143014000-143015600	Genic enhancers	A549	lung
37	chr4:143014000-143016400	Weak transcription	HUVEC	blood vessel
38	chr4:143014000-143016600	Strong transcription	NHEK	skin
39	chr4:143014000-143016800	Strong transcription	HSMM	muscle
40	chr4:143014000-143017600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:143014000-143017600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:143014000-143035800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:143014200-143016400	Weak transcription	Primary T cells from cord blood	blood
44	chr4:143014200-143016600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:143014200-143021800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:143014400-143015400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:143014400-143015400	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:143014400-143022600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:143014600-143016400	Weak transcription	NHDF-Ad	bronchial
50	chr4:143014600-143016600	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links