Variant report

Variant	rs12030730
Chromosome Location	chr1:85454109-85454110
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10443172	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs11588160	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12024977	0.93[JPT][hapmap]
rs12030837	1.00[JPT][hapmap]
rs12037219	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12042018	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042845	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12042910	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12045710	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1371140	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1371141	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1371142	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1371143	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837329	0.83[ASN][1000 genomes]
rs1853776	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028304	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs2083283	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2083284	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304641	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2840050	0.86[JPT][hapmap]
rs55721024	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61768850	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61768852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61768853	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61768854	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6665436	0.93[JPT][hapmap]
rs6672362	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679539	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs6680422	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6688354	0.86[CEU][hapmap]
rs6690464	0.86[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs6690583	0.86[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs6699356	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699956	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7522239	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs7540706	0.85[CEU][hapmap]
rs7547224	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7547317	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs893620	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs898036	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	esv3515392	chr1:85437980-85465392	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3515393	chr1:85437980-85465392	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3372619	chr1:85451989-85454537	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
9	esv3441134	chr1:85452214-85454337	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85441200-85460200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:85450800-85454800	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:85453600-85454400	Enhancers	Primary B cells from cord blood	blood
4	chr1:85453600-85454800	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr1:85453800-85454200	Enhancers	GM12878-XiMat	blood
6	chr1:85453800-85454800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:85453800-85454800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr1:85453800-85454800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:85453800-85454800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr1:85453800-85455000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:85454000-85454800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:85454000-85454800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr1:85454000-85454800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:85454000-85454800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:85454000-85455200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links