Variant report

Variant	rs2107449
Chromosome Location	chr7:21488929-21488930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1011167	0.96[GIH][hapmap];0.95[TSI][hapmap]
rs1018954	0.85[JPT][hapmap]
rs1989985	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2282901	0.80[TSI][hapmap]
rs2390535	0.80[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2390536	0.80[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2390538	0.82[LWK][hapmap]
rs28446999	0.81[AMR][1000 genomes]
rs55825095	0.84[AMR][1000 genomes]
rs6966442	0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.86[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	nsv1027302	chr7:21391598-21727016	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv538800	chr7:21391598-21727016	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1028434	chr7:21468437-21636671	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1023655	chr7:21486485-21727016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538801	chr7:21486485-21727016	ZNF genes & repeats Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2107449	RAPGEF5	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21468400-21490600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:21468400-21497800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:21468600-21495600	Weak transcription	Fetal Intestine Large	intestine
4	chr7:21468800-21489000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:21468800-21493600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:21470000-21490400	Weak transcription	Fetal Kidney	kidney
7	chr7:21470000-21497800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr7:21470200-21490600	Weak transcription	Psoas Muscle	Psoas
9	chr7:21470200-21494400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr7:21470400-21490600	Weak transcription	Pancreas	Pancrea
11	chr7:21470400-21494600	Weak transcription	Fetal Stomach	stomach
12	chr7:21470400-21516600	Weak transcription	Liver	Liver
13	chr7:21470400-21536400	Weak transcription	Esophagus	oesophagus
14	chr7:21470600-21490800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr7:21472000-21489800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:21472000-21495200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr7:21472000-21495200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr7:21472800-21490400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:21472800-21490400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr7:21472800-21490600	Weak transcription	Left Ventricle	heart
21	chr7:21472800-21490600	Weak transcription	Lung	lung
22	chr7:21472800-21492000	Weak transcription	Small Intestine	intestine
23	chr7:21472800-21506000	Weak transcription	Right Ventricle	heart
24	chr7:21473600-21489600	Weak transcription	Fetal Brain Male	brain
25	chr7:21474200-21493400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:21474800-21497200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr7:21474800-21520600	Weak transcription	Brain Angular Gyrus	brain
28	chr7:21476200-21493200	Weak transcription	Brain Anterior Caudate	brain
29	chr7:21476400-21492400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:21480800-21490000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:21481000-21490400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr7:21484000-21493600	Weak transcription	Fetal Lung	lung
33	chr7:21484200-21489800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr7:21484400-21490000	Weak transcription	HUVEC	blood vessel
35	chr7:21485400-21495200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr7:21485600-21489600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr7:21486000-21490800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr7:21486800-21490600	Weak transcription	Ovary	ovary
39	chr7:21487400-21490600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr7:21487400-21557000	Weak transcription	Aorta	Aorta
41	chr7:21487600-21490000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr7:21487600-21498400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr7:21487800-21491000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:21488000-21489000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr7:21488000-21489000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr7:21488000-21490400	Strong transcription	Primary B cells from cord blood	blood
47	chr7:21488200-21495800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
48	chr7:21488400-21489000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr7:21488400-21489000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
50	chr7:21488400-21489000	Enhancers	Primary T helper cells PMA-I stimulated	--

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