Variant report

Variant	rs1366223
Chromosome Location	chr5:177648488-177648489
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2913746	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2913863	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2913868	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2961678	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2961683	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3812089	0.82[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.97[ASN][1000 genomes]
rs62388715	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1366223	UNC5A	cis	parietal	SCAN
rs1366223	MXD3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177634000-177650800	Strong transcription	Placenta	Placenta
2	chr5:177634400-177654200	Strong transcription	Fetal Stomach	stomach
3	chr5:177635000-177650200	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:177635000-177650400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:177635000-177650400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:177635000-177650400	Strong transcription	Adipose Nuclei	Adipose
7	chr5:177635400-177649200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:177635400-177651000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:177635800-177657000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:177636000-177654000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:177639400-177657600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:177640000-177650400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:177640400-177655600	Weak transcription	Right Atrium	heart
14	chr5:177641000-177650800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:177642600-177654200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:177643200-177651000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:177643400-177649400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:177643400-177650200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:177643400-177650600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:177643400-177651600	Weak transcription	HSMMtube	muscle
21	chr5:177643400-177656400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:177643600-177649600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:177643600-177650400	Weak transcription	Fetal Heart	heart
24	chr5:177643600-177654400	Weak transcription	Aorta	Aorta
25	chr5:177643600-177655200	Weak transcription	Stomach Mucosa	stomach
26	chr5:177643800-177648600	Weak transcription	Brain Substantia Nigra	brain
27	chr5:177643800-177650200	Weak transcription	HMEC	breast
28	chr5:177643800-177652200	Strong transcription	Liver	Liver
29	chr5:177643800-177653800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:177644000-177649400	Weak transcription	Psoas Muscle	Psoas
31	chr5:177644000-177650000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:177644000-177651400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:177644200-177654800	Weak transcription	NHDF-Ad	bronchial
34	chr5:177644400-177649000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:177644600-177648800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:177645200-177649200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:177645200-177649600	Strong transcription	Fetal Lung	lung
38	chr5:177645400-177650200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:177645400-177651400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr5:177645400-177651600	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr5:177645400-177654800	Strong transcription	Hela-S3	cervix
42	chr5:177645400-177656800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr5:177645400-177656800	Strong transcription	Dnd41	blood
44	chr5:177645600-177654800	Weak transcription	HSMM	muscle
45	chr5:177645800-177648600	Weak transcription	GM12878-XiMat	blood
46	chr5:177645800-177650000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:177646000-177651400	Weak transcription	NH-A	brain
48	chr5:177646000-177654400	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:177646200-177648800	Weak transcription	HepG2	liver
50	chr5:177646200-177654000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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