Variant report

Variant	rs11119934
Chromosome Location	chr1:212603790-212603791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr1:212602804-212605297	K562	blood:	n/a	chr1:212604609-212604625
2	NR2F2	chr1:212603243-212603843	K562	blood:	n/a	n/a
3	NR2F2	chr1:212603431-212604960	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
2	chr1:212601033..212604167-chr1:212605917..212607600,3	MCF-7	breast:
3	chr1:212601837..212604261-chr1:212607082..212608866,2	K562	blood:

Variant related genes	Relation type
NENF	TF binding region
ENSG00000065600	Chromatin interaction
ENSG00000117691	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1056985	0.93[CEU][hapmap];0.95[CHB][hapmap]
rs10863965	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863966	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs11119891	0.93[CEU][hapmap]
rs11119910	0.81[CEU][hapmap]
rs11119918	0.95[CHB][hapmap]
rs11119927	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119932	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119936	0.81[ASN][1000 genomes]
rs12031941	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12033979	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12119779	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12128965	0.93[CEU][hapmap];0.95[CHB][hapmap]
rs12133582	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133636	0.95[CHB][hapmap]
rs12134599	0.95[CHB][hapmap]
rs12136095	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs12141427	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12143853	0.91[CEU][hapmap]
rs12145170	0.85[EUR][1000 genomes]
rs12145377	0.83[CEU][hapmap]
rs12145484	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs12239580	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12403586	0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1342152	0.93[CEU][hapmap];0.95[CHB][hapmap]
rs1388033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388034	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14123	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap]
rs17018847	0.92[CEU][hapmap]
rs17018853	0.92[CEU][hapmap]
rs17666015	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs1808986	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1826214	0.85[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2166155	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2298115	0.93[CEU][hapmap];0.95[CHB][hapmap]
rs3754144	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3767867	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3767868	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs3820513	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4338424	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4548507	0.87[ASN][1000 genomes]
rs4951596	1.00[ASN][1000 genomes]
rs4951597	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828751	0.89[EUR][1000 genomes]
rs74138154	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903119	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11119934	PPP2R5A	cis	Whole Blood	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212591000-212605600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:212598400-212605600	Weak transcription	Brain Substantia Nigra	brain
3	chr1:212598600-212603800	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:212598800-212603800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:212598800-212605600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:212602800-212604800	Weak transcription	Placenta	Placenta
7	chr1:212602800-212605600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:212603400-212604000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:212603400-212605600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:212603400-212606000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:212603600-212603800	Enhancers	Brain Cingulate Gyrus	brain
12	chr1:212603600-212603800	Enhancers	NHLF	lung
13	chr1:212603600-212604000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:212603600-212604000	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links