Variant report

Variant	rs2158883
Chromosome Location	chr7:22389792-22389793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:22377860..22380103-chr7:22388020..22389955,2	K562	blood:
2	chr7:22388247..22390670-chr7:22394895..22396584,2	MCF-7	breast:
3	chr7:22389519..22393797-chr7:22394454..22398682,6	K562	blood:
4	chr7:22385617..22387742-chr7:22389122..22391158,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136237	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10499549	0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12668119	0.82[AFR][1000 genomes]
rs1859740	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1859741	0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1859742	0.92[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2108288	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722129	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56392704	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73683358	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7785857	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7798524	0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830923	chr7:22316841-22494973	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1792359	chr7:22377636-22391198	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2158883	RAPGEF5	cis	lymphoblastoid	seeQTL
rs2158883	RAPGEF5	cis	multi-tissue	Pritchard

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:22369400-22394800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:22370200-22390400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:22380000-22392200	Weak transcription	Primary B cells from cord blood	blood
4	chr7:22381800-22390200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr7:22382000-22390000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr7:22382000-22390200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:22382000-22390200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:22383000-22395200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:22384200-22395800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:22384800-22395000	Weak transcription	Thymus	Thymus
11	chr7:22385800-22391600	Weak transcription	Fetal Thymus	thymus
12	chr7:22386400-22390000	Weak transcription	Osteobl	bone
13	chr7:22386400-22390200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:22386600-22390000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:22386600-22390400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:22386800-22390200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:22387600-22389800	Enhancers	K562	blood
18	chr7:22388400-22389800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:22388400-22390200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:22388400-22390200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr7:22388400-22390200	Weak transcription	HMEC	breast
22	chr7:22388400-22390200	Weak transcription	NHEK	skin
23	chr7:22388400-22395000	Weak transcription	Esophagus	oesophagus
24	chr7:22388600-22390200	Enhancers	HepG2	liver
25	chr7:22388600-22390400	Weak transcription	Stomach Mucosa	stomach
26	chr7:22388600-22391400	Weak transcription	Pancreas	Pancrea
27	chr7:22389000-22392800	Enhancers	Fetal Intestine Large	intestine
28	chr7:22389400-22390000	Enhancers	Duodenum Mucosa	Duodenum
29	chr7:22389400-22391200	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr7:22389400-22391600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr7:22389400-22392200	Enhancers	Fetal Intestine Small	intestine
32	chr7:22389400-22392400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:22389400-22392600	Flanking Active TSS	GM12878-XiMat	blood
34	chr7:22389600-22390000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr7:22389600-22391000	Genic enhancers	Dnd41	blood
36	chr7:22389600-22391200	Enhancers	HUVEC	blood vessel
37	chr7:22389600-22391600	Enhancers	Liver	Liver
38	chr7:22389600-22392600	Weak transcription	Small Intestine	intestine

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