Variant report

Variant	rs6545043
Chromosome Location	chr2:48723552-48723553
allele	A/G
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];0.98[ASN][1000 genomes]
rs10185212	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11125172	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11677398	1.00[CEU][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11695461	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12477901	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[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]
rs4328683	1.00[CEU][hapmap]
rs4371401	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]
rs4429520	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4430989	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4464333	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs4953582	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4953584	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[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];0.87[ASN][1000 genomes]
rs4953588	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[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]
rs6545042	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545044	1.00[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6715766	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6744619	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6756820	1.00[CEU][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]
rs7557764	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7608588	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];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	chr2:48673200-48724000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:48689200-48735600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:48690000-48735600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:48694000-48729400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
6	chr2:48695200-48723800	Weak transcription	Gastric	stomach
7	chr2:48695200-48725800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:48695200-48728000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:48695400-48728000	Weak transcription	Hela-S3	cervix
10	chr2:48695600-48735200	Weak transcription	K562	blood
11	chr2:48696400-48723800	Weak transcription	Aorta	Aorta
12	chr2:48698800-48729200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:48698800-48735400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:48700200-48735400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:48700600-48735600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr2:48703200-48729800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:48704000-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:48704400-48730000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr2:48704600-48735400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:48704600-48735600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:48706600-48728000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:48707400-48742000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:48707600-48725800	Weak transcription	Small Intestine	intestine
24	chr2:48707600-48725800	Weak transcription	HMEC	breast
25	chr2:48707800-48725600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:48708000-48724600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:48708000-48725800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:48708400-48725600	Weak transcription	Pancreas	Pancrea
29	chr2:48708400-48735400	Weak transcription	Stomach Mucosa	stomach
30	chr2:48709400-48755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:48710200-48745000	Weak transcription	Fetal Brain Male	brain
32	chr2:48710400-48735400	Weak transcription	NHLF	lung
33	chr2:48710800-48725600	Weak transcription	HUVEC	blood vessel
34	chr2:48711400-48723800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:48711400-48725800	Weak transcription	Fetal Kidney	kidney
36	chr2:48711600-48723800	Weak transcription	NH-A	brain
37	chr2:48711600-48725600	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:48712000-48723800	Weak transcription	Ovary	ovary
39	chr2:48712000-48725600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:48712000-48728200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:48712400-48734200	Weak transcription	NHEK	skin
42	chr2:48713000-48729000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:48714000-48725600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:48714000-48725600	Weak transcription	HSMMtube	muscle
45	chr2:48714200-48723800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr2:48714200-48724000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:48714200-48725600	Weak transcription	HepG2	liver
48	chr2:48714400-48727200	Weak transcription	HSMM	muscle
49	chr2:48714400-48735400	Weak transcription	Brain Germinal Matrix	brain
50	chr2:48714800-48724000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links