Variant report

Variant	rs1859741
Chromosome Location	chr7:22391198-22391199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:22386235..22387769-chr7:22390582..22392428,2	MCF-7	breast:
2	chr7:22383332..22385281-chr7:22391163..22392665,3	K562	blood:
3	chr7:22390336..22392269-chr7:22472031..22473610,2	MCF-7	breast:
4	chr7:22389519..22393797-chr7:22394454..22398682,6	K562	blood:
5	chr7:22383521..22386043-chr7:22390326..22392664,3	K562	blood:

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	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17146725	0.85[CEU][hapmap]
rs1859740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108288	0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2158882	0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2158883	0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4722129	0.91[ASN][1000 genomes]
rs4722130	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs56392704	0.91[ASN][1000 genomes]
rs73683358	0.89[ASN][1000 genomes]
rs7785857	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7798524	1.00[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[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs1859741	RAPGEF5	cis	lymphoblastoid	seeQTL
rs1859741	RAPGEF5	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 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	chr7:22380000-22392200	Weak transcription	Primary B cells from cord blood	blood
3	chr7:22383000-22395200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:22384200-22395800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:22384800-22395000	Weak transcription	Thymus	Thymus
6	chr7:22385800-22391600	Weak transcription	Fetal Thymus	thymus
7	chr7:22388400-22395000	Weak transcription	Esophagus	oesophagus
8	chr7:22388600-22391400	Weak transcription	Pancreas	Pancrea
9	chr7:22389000-22392800	Enhancers	Fetal Intestine Large	intestine
10	chr7:22389400-22391200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr7:22389400-22391600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr7:22389400-22392200	Enhancers	Fetal Intestine Small	intestine
13	chr7:22389400-22392400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:22389400-22392600	Flanking Active TSS	GM12878-XiMat	blood
15	chr7:22389600-22391200	Enhancers	HUVEC	blood vessel
16	chr7:22389600-22391600	Enhancers	Liver	Liver
17	chr7:22389600-22392600	Weak transcription	Small Intestine	intestine
18	chr7:22389800-22391200	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr7:22389800-22391200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr7:22389800-22391200	Flanking Active TSS	K562	blood
21	chr7:22389800-22391400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr7:22389800-22391600	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr7:22390000-22391600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr7:22390000-22391800	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr7:22390000-22391800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr7:22390000-22392000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:22390000-22392000	Enhancers	Osteobl	bone
28	chr7:22390000-22392200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:22390200-22391200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr7:22390200-22391200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:22390200-22391600	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr7:22390200-22391600	Enhancers	HMEC	breast
33	chr7:22390200-22391800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:22390200-22391800	Flanking Active TSS	HepG2	liver
35	chr7:22390200-22392000	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr7:22390200-22392000	Enhancers	NHEK	skin
37	chr7:22390400-22391200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr7:22390400-22391800	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr7:22390400-22391800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr7:22390400-22392600	Enhancers	Stomach Mucosa	stomach
41	chr7:22390600-22391200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:22390600-22395200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr7:22390800-22395000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr7:22391000-22391600	Flanking Active TSS	Dnd41	blood

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