Variant report

Variant	rs2913752
Chromosome Location	chr5:177636571-177636572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:177593389..177595901-chr5:177636350..177639328,2	MCF-7	breast:
2	chr4:26581090..26582592-chr5:177636048..177637603,2	K562	blood:
3	chr5:177634469..177636914-chr5:178050072..178052973,2	K562	blood:

Variant related genes	Relation type
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17639067	0.91[YRI][hapmap]
rs2913747	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2913749	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2913753	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2913862	0.94[ASN][1000 genomes]
rs2913864	0.94[ASN][1000 genomes]
rs2913865	0.94[ASN][1000 genomes]
rs2913867	0.92[ASN][1000 genomes]
rs2961674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][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]
rs2961676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2961677	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2961679	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2961682	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2961685	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2961686	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9329138	0.83[AMR][1000 genomes];0.95[EUR][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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	106 gene(s)	inside rSNPs	diseases
5	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2913752	RAB24	cis	parietal	SCAN
rs2913752	UNC5A	cis	parietal	SCAN
rs2913752	CNOT6	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177632600-177636600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
2	chr5:177633000-177643000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:177633400-177636600	Genic enhancers	Gastric	stomach
4	chr5:177633600-177639600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:177633600-177643200	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr5:177633600-177644000	Genic enhancers	Fetal Intestine Large	intestine
7	chr5:177633800-177636600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
8	chr5:177633800-177640000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:177633800-177641600	Strong transcription	Primary B cells from cord blood	blood
10	chr5:177633800-177642600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr5:177633800-177643400	Genic enhancers	Fetal Intestine Small	intestine
12	chr5:177633800-177643600	Strong transcription	Aorta	Aorta
13	chr5:177633800-177644000	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr5:177634000-177643800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:177634000-177644000	Strong transcription	Rectal Smooth Muscle	rectum
16	chr5:177634000-177650800	Strong transcription	Placenta	Placenta
17	chr5:177634200-177640600	Strong transcription	HSMMtube	muscle
18	chr5:177634200-177643000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:177634200-177644000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:177634400-177637400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:177634400-177643200	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr5:177634400-177643600	Strong transcription	Brain Angular Gyrus	brain
23	chr5:177634400-177643800	Strong transcription	Colon Smooth Muscle	Colon
24	chr5:177634400-177654200	Strong transcription	Fetal Stomach	stomach
25	chr5:177634600-177637600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:177634600-177640200	Strong transcription	Brain Hippocampus Middle	brain
27	chr5:177634600-177641600	Strong transcription	Fetal Brain Male	brain
28	chr5:177634600-177642400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr5:177634600-177643000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:177634600-177643200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:177634600-177643600	Strong transcription	Brain Cingulate Gyrus	brain
32	chr5:177634600-177644200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr5:177634600-177644400	Strong transcription	Fetal Lung	lung
34	chr5:177634600-177646000	Strong transcription	Thymus	Thymus
35	chr5:177634800-177642800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:177634800-177645800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:177635000-177639600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:177635000-177639800	Weak transcription	Right Atrium	heart
39	chr5:177635000-177642400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr5:177635000-177643800	Strong transcription	Fetal Kidney	kidney
41	chr5:177635000-177644000	Strong transcription	Brain Anterior Caudate	brain
42	chr5:177635000-177647000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:177635000-177650200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:177635000-177650400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:177635000-177650400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:177635000-177650400	Strong transcription	Adipose Nuclei	Adipose
47	chr5:177635200-177637000	Genic enhancers	Dnd41	blood
48	chr5:177635200-177638200	Strong transcription	Liver	Liver
49	chr5:177635200-177639600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:177635200-177639600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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