Variant report

Variant	rs4371401
Chromosome Location	chr2:48727280-48727281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10164898	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10185212	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11125172	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11677398	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11695461	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12477901	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13386132	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3811520	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4328683	1.00[CEU][hapmap]
rs4429520	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4430989	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4464333	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4564825	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4952913	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4953582	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4953584	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs4953585	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4953586	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4953588	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6545040	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6545042	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545043	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545044	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6715766	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6744619	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6756820	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs7355307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7557764	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7608588	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48689200-48735600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:48690000-48735600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:48694000-48729400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
5	chr2:48695200-48728000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:48695400-48728000	Weak transcription	Hela-S3	cervix
7	chr2:48695600-48735200	Weak transcription	K562	blood
8	chr2:48698800-48729200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:48698800-48735400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:48700200-48735400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:48700600-48735600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:48703200-48729800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:48704000-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:48704400-48730000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr2:48704600-48735400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:48704600-48735600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:48706600-48728000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:48707400-48742000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:48708400-48735400	Weak transcription	Stomach Mucosa	stomach
20	chr2:48709400-48755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:48710200-48745000	Weak transcription	Fetal Brain Male	brain
22	chr2:48710400-48735400	Weak transcription	NHLF	lung
23	chr2:48712000-48728200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:48712400-48734200	Weak transcription	NHEK	skin
25	chr2:48713000-48729000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:48714400-48735400	Weak transcription	Brain Germinal Matrix	brain
27	chr2:48717200-48728000	Weak transcription	Esophagus	oesophagus
28	chr2:48717800-48729600	Strong transcription	Primary B cells from cord blood	blood
29	chr2:48717800-48733200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:48720400-48729800	Strong transcription	Liver	Liver
31	chr2:48720800-48729800	Strong transcription	Primary T cells from cord blood	blood
32	chr2:48720800-48735800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:48721000-48735600	Strong transcription	Fetal Thymus	thymus
34	chr2:48721000-48736400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:48721600-48731400	Strong transcription	Fetal Stomach	stomach
36	chr2:48721800-48729000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:48721800-48729600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:48721800-48729600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr2:48722000-48727400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:48722000-48729800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:48722200-48728800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:48722200-48729600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:48722600-48741800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:48722800-48729600	Strong transcription	Brain Anterior Caudate	brain
45	chr2:48723200-48728800	Strong transcription	Fetal Brain Female	brain
46	chr2:48723200-48729800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr2:48723200-48730000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:48723400-48729600	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr2:48723800-48748200	Strong transcription	GM12878-XiMat	blood
50	chr2:48724000-48728400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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