Variant report

Variant	rs3890801
Chromosome Location	chr1:212813503-212813504
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	chr1:212813465..212815464-chr1:212818635..212821211,2	K562	blood:
2	chr1:212808458..212810460-chr1:212812448..212814204,2	K562	blood:

Variant related genes	Relation type
ENSG00000226036	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11571532	1.00[ASN][1000 genomes]
rs11571536	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11571538	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11571552	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs17019442	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2501840	0.90[CEU][hapmap]
rs3123539	0.81[CEU][hapmap]
rs35777725	1.00[ASN][1000 genomes]
rs55854080	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56023947	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6540751	1.00[ASN][1000 genomes]
rs6656504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670396	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6682816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72756370	1.00[ASN][1000 genomes]
rs72756371	1.00[ASN][1000 genomes]
rs74138596	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138599	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138601	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551520	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212802600-212822800	Weak transcription	Fetal Kidney	kidney
2	chr1:212810800-212813600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:212810800-212813800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:212811000-212816800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:212812000-212814000	Enhancers	NHLF	lung
6	chr1:212812400-212821800	Weak transcription	Fetal Lung	lung
7	chr1:212812800-212813600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:212812800-212817400	Weak transcription	Thymus	Thymus
9	chr1:212812800-212819200	Weak transcription	Lung	lung
10	chr1:212813000-212813800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:212813000-212817200	Weak transcription	Fetal Thymus	thymus
12	chr1:212813200-212813800	Bivalent Enhancer	NHDF-Ad	bronchial
13	chr1:212813400-212814200	ZNF genes & repeats	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links