Variant report

Variant	rs1258072
Chromosome Location	chr1:47098048-47098049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47096461..47099303-chr1:47102647..47105072,2	K562	blood:
2	chr1:47081101..47083522-chr1:47096778..47098281,2	K562	blood:

Variant related genes	Relation type
ENSG00000142961	Chromatin interaction
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10890410	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs10890414	0.83[ASN][1000 genomes]
rs11211332	0.89[EUR][1000 genomes]
rs11211343	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11801744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs12059860	1.00[CEU][hapmap]
rs12562113	0.82[ASN][1000 genomes]
rs12566278	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12568734	0.83[ASN][1000 genomes]
rs1258010	1.00[TSI][hapmap]
rs1258022	1.00[TSI][hapmap]
rs1258055	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1258058	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258063	0.95[ASN][1000 genomes]
rs1258064	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258065	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258066	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258068	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1268714	0.98[ASN][1000 genomes]
rs1273237	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13374909	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1745376	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1933932	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2146560	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2181412	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241863	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2241864	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439442	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2476153	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2476155	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2476156	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2476157	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2476159	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2486160	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2486162	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3011290	0.83[ASN][1000 genomes]
rs3737742	1.00[TSI][hapmap]
rs3766218	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766221	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3766222	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3766223	0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56771521	0.83[ASN][1000 genomes]
rs57495753	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs582269	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs582323	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582760	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs583649	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58678760	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59479990	0.83[ASN][1000 genomes]
rs596794	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs597221	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs604233	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs604264	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs611919	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs629412	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs631368	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs631840	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636082	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs636122	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636424	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs648822	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs654544	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs655369	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs657166	0.90[ASN][1000 genomes]
rs6677350	1.00[CEU][hapmap]
rs669647	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs673134	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs675731	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs678466	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs683585	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs685862	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes]
rs689300	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs723333	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724309	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs72896683	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72900715	0.83[ASN][1000 genomes]
rs736188	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9094	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1007280	chr1:47088116-47129588	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47083000-47100000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:47083200-47100200	Weak transcription	Psoas Muscle	Psoas
3	chr1:47083200-47104600	Weak transcription	Stomach Mucosa	stomach
4	chr1:47083200-47115000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:47083400-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:47085600-47099000	Weak transcription	GM12878-XiMat	blood
7	chr1:47088000-47100800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:47088200-47100000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:47088200-47100000	Weak transcription	Spleen	Spleen
10	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:47088600-47108600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:47088600-47108800	Weak transcription	Hela-S3	cervix
13	chr1:47089800-47112400	Weak transcription	Small Intestine	intestine
14	chr1:47090200-47121400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:47091000-47099800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:47091400-47105000	Weak transcription	HMEC	breast
17	chr1:47091600-47100800	Weak transcription	Fetal Kidney	kidney
18	chr1:47093600-47100000	Weak transcription	Lung	lung
19	chr1:47094200-47101600	Strong transcription	Left Ventricle	heart
20	chr1:47094200-47102600	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:47094200-47102600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr1:47094200-47103400	Strong transcription	Fetal Muscle Leg	muscle
23	chr1:47094200-47105800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:47094400-47102400	Strong transcription	Brain Angular Gyrus	brain
25	chr1:47094400-47103800	Strong transcription	Primary T cells from cord blood	blood
26	chr1:47094600-47102600	Strong transcription	Adipose Nuclei	Adipose
27	chr1:47094600-47105600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:47094600-47111000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr1:47094600-47119200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:47095200-47107800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:47095400-47103600	Strong transcription	Liver	Liver
32	chr1:47095600-47102200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:47095600-47103000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:47095600-47103000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr1:47095600-47103000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr1:47095600-47103200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:47095600-47104000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:47095600-47109000	Strong transcription	Placenta	Placenta
39	chr1:47095800-47100000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:47095800-47104600	Weak transcription	A549	lung
41	chr1:47096000-47103400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:47096400-47100600	Weak transcription	HUVEC	blood vessel
43	chr1:47096400-47103200	Strong transcription	Fetal Brain Female	brain
44	chr1:47096600-47098400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:47096600-47098400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:47096600-47100200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:47096600-47101600	Strong transcription	Right Ventricle	heart
48	chr1:47096600-47101800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:47096600-47103800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:47096600-47105800	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links