Variant report

Variant	rs3806749
Chromosome Location	chr4:56830934-56830935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10212814	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10866430	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11133419	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11724411	0.94[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11726419	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11731842	0.94[CEU][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11732545	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11734217	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11933720	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11934142	0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11937929	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11945709	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12642567	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12645491	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13112832	0.80[EUR][1000 genomes]
rs13121634	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13127483	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13129197	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17797425	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.80[EUR][1000 genomes]
rs2290014	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28472524	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28507080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28610174	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3214045	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34285861	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35003282	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35123416	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35814086	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4499751	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62308565	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308614	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62308621	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6814923	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6815354	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6830668	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6838426	0.81[YRI][hapmap]
rs6849999	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7670026	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9312668	1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[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	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3406311	chr4:56580578-56840877	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56815800-56839200	Weak transcription	Esophagus	oesophagus
2	chr4:56815800-56875000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:56816000-56833400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:56816200-56839400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:56816200-56846600	Weak transcription	Right Ventricle	heart
6	chr4:56816200-56873400	Weak transcription	Pancreas	Pancrea
7	chr4:56816200-56884200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:56816200-56887800	Weak transcription	Gastric	stomach
9	chr4:56816400-56866000	Weak transcription	Spleen	Spleen
10	chr4:56816400-56890800	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:56816600-56831800	Weak transcription	Fetal Lung	lung
12	chr4:56816600-56834000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:56816600-56851800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:56816600-56852000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:56816600-56865800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:56816600-56890600	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:56816600-56896400	Weak transcription	Fetal Heart	heart
18	chr4:56816800-56831400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:56816800-56865800	Weak transcription	Small Intestine	intestine
20	chr4:56816800-56869800	Weak transcription	HepG2	liver
21	chr4:56817400-56839200	Weak transcription	NHEK	skin
22	chr4:56817400-56885400	Weak transcription	NHDF-Ad	bronchial
23	chr4:56817800-56846200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr4:56817800-56854600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:56818200-56837200	Strong transcription	Fetal Thymus	thymus
26	chr4:56818200-56853800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:56818400-56831000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:56818400-56833000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr4:56818800-56841800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:56819000-56835400	Strong transcription	Dnd41	blood
31	chr4:56819000-56897400	Weak transcription	HSMMtube	muscle
32	chr4:56819200-56859600	Weak transcription	Fetal Kidney	kidney
33	chr4:56819200-56890600	Weak transcription	NHLF	lung
34	chr4:56820000-56841600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:56820600-56892400	Weak transcription	Hela-S3	cervix
36	chr4:56821600-56831400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:56822200-56849800	Weak transcription	Fetal Brain Male	brain
38	chr4:56822200-56873600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr4:56822400-56845000	Weak transcription	K562	blood
40	chr4:56822400-56865800	Weak transcription	Psoas Muscle	Psoas
41	chr4:56823600-56893800	Weak transcription	HMEC	breast
42	chr4:56824000-56846600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:56824200-56832000	Weak transcription	Liver	Liver
44	chr4:56824200-56834200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:56824600-56838400	Weak transcription	Fetal Brain Female	brain
46	chr4:56824600-56839600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:56824600-56846800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:56824600-56846800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:56824800-56831400	Weak transcription	Placenta	Placenta
50	chr4:56825200-56831800	Weak transcription	Ovary	ovary

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