Variant report

Variant	rs59877390
Chromosome Location	chr1:212855254-212855255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212782111..212784308-chr1:212852727..212855558,2	MCF-7	breast:
2	chr1:212851040..212855618-chr1:212856353..212859707,5	MCF-7	breast:
3	chr1:212780750..212783625-chr1:212854887..212857675,2	K562	blood:
4	chr1:212847538..212850191-chr1:212852338..212855391,3	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12726783	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12754070	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17019553	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17019556	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35027464	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4026627	1.00[ASN][1000 genomes]
rs55846918	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56283090	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59691875	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59746440	0.95[ASN][1000 genomes]
rs72756401	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72758412	0.95[ASN][1000 genomes]
rs882410	0.95[ASN][1000 genomes]
rs906363	1.00[ASN][1000 genomes]
rs906364	0.81[AFR][1000 genomes]
rs9658807	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
5	esv1829918	chr1:212828460-212874731	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212851600-212856200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:212851600-212856800	Weak transcription	Fetal Thymus	thymus
3	chr1:212851800-212856000	Weak transcription	Adipose Nuclei	Adipose
4	chr1:212851800-212856800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:212852200-212855400	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:212852200-212855400	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:212852400-212855400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:212852600-212855400	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr1:212852600-212856200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:212852800-212855400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:212852800-212856000	Weak transcription	Spleen	Spleen
12	chr1:212853000-212855800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr1:212853200-212855400	Enhancers	GM12878-XiMat	blood
14	chr1:212853800-212860000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:212854000-212855600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:212854200-212855600	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr1:212854200-212856000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:212854400-212855600	Weak transcription	Liver	Liver
19	chr1:212854600-212856800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:212855000-212856000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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