Variant report

Variant	rs2812222
Chromosome Location	chr13:50714998-50714999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50696397..50701500-chr13:50709372..50715454,8	K562	blood:
2	chr13:50696811..50698790-chr13:50714697..50717058,2	K562	blood:
3	chr13:50698440..50700392-chr13:50713027..50715601,3	MCF-7	breast:
4	chr13:50707603..50710075-chr13:50713599..50715731,3	K562	blood:
5	chr13:50708042..50711233-chr13:50714851..50719539,6	K562	blood:
6	chr13:50698530..50704909-chr13:50711200..50717367,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1326120	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2066557	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2066558	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2066572	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2066575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2066587	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066591	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066594	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2687950	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2687951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2740508	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2740524	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2740544	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2740545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2760914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2803839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2812204	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812216	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812217	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2997624	0.85[AMR][1000 genomes]
rs4942899	0.81[AMR][1000 genomes]
rs4942901	0.94[AMR][1000 genomes]
rs7338055	0.81[AMR][1000 genomes]
rs790943	0.86[CHB][hapmap]
rs9568363	0.91[AMR][1000 genomes]
rs9568364	0.91[AMR][1000 genomes]
rs9568366	0.90[CHB][hapmap]
rs9596215	0.89[AMR][1000 genomes]
rs9596219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9596220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1041501	chr13:50683189-50795195	Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv900076	chr13:50710579-50912578	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2812222	DLEU2	Cis_1M	lymphoblastoid	RTeQTL
rs2812222	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50713600-50715000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:50714000-50715000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
3	chr13:50714000-50715200	Enhancers	Brain Hippocampus Middle	brain
4	chr13:50714000-50715800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr13:50714000-50716200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:50714000-50716200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:50714200-50715000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr13:50714200-50715200	Enhancers	Brain Cingulate Gyrus	brain
9	chr13:50714200-50715400	Enhancers	Adipose Nuclei	Adipose
10	chr13:50714200-50715800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:50714200-50715800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:50714200-50715800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr13:50714200-50716200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:50714400-50715200	Enhancers	Brain Angular Gyrus	brain
15	chr13:50714400-50715600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr13:50714400-50715600	Enhancers	Fetal Brain Male	brain
17	chr13:50714400-50715800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr13:50714400-50716000	Enhancers	NHLF	lung
19	chr13:50714600-50715000	Enhancers	Fetal Lung	lung
20	chr13:50714600-50715800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr13:50714600-50716000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr13:50714600-50716400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr13:50714800-50715000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr13:50714800-50715000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr13:50714800-50715200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr13:50714800-50715200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr13:50714800-50715600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:50714800-50716000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:50714800-50716400	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links