Variant report

Variant	rs1632597
Chromosome Location	chr5:1875037-1875038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1032436	0.92[CEU][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs1038563	0.89[EUR][1000 genomes]
rs1532272	0.95[JPT][hapmap]
rs1684968	0.87[EUR][1000 genomes]
rs1689718	0.86[ASN][1000 genomes]
rs260402	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2631800	0.89[EUR][1000 genomes]
rs4501375	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4643997	0.82[EUR][1000 genomes]
rs6876836	0.86[ASN][1000 genomes]
rs7711597	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7719948	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7728559	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7733198	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7734041	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv596891	chr5:1822326-1880891	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv880647	chr5:1822326-1880891	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv881619	chr5:1822326-1886471	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv881557	chr5:1822326-1932463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv596892	chr5:1832240-1892759	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1019713	chr5:1833072-1884738	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv596893	chr5:1839498-1892759	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1018082	chr5:1849721-1884738	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv881470	chr5:1850563-1892759	Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv881188	chr5:1852284-1892759	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1632597	IRX2	cis	cerebellum	SCAN
rs1632597	CLPTM1L	cis	cerebellum	SCAN
rs1632597	PRSS45	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1856000-1875400	Weak transcription	Right Atrium	heart
2	chr5:1873400-1875600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:1873400-1876000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
4	chr5:1873400-1876400	Bivalent Enhancer	Fetal Intestine Small	intestine
5	chr5:1874400-1877400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
6	chr5:1874600-1875200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:1874600-1875600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr5:1874600-1875800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:1874600-1876000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr5:1874600-1876000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr5:1874600-1876000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr5:1874600-1876400	Bivalent Enhancer	Fetal Stomach	stomach
13	chr5:1874600-1876600	Bivalent Enhancer	Fetal Brain Male	brain
14	chr5:1874600-1877200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
15	chr5:1874600-1877200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr5:1874800-1875400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:1874800-1875600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr5:1874800-1877400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr5:1875000-1875200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:1875000-1875200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
21	chr5:1875000-1875200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
22	chr5:1875000-1875200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
23	chr5:1875000-1875200	Bivalent Enhancer	Stomach Mucosa	stomach
24	chr5:1875000-1875200	Bivalent Enhancer	A549	lung
25	chr5:1875000-1875400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr5:1875000-1875400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:1875000-1875800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
28	chr5:1875000-1876000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:1875000-1876000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr5:1875000-1876000	Bivalent Enhancer	Spleen	Spleen
31	chr5:1875000-1876200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:1875000-1876200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:1875000-1876200	Bivalent Enhancer	Fetal Muscle Leg	muscle
34	chr5:1875000-1876400	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:1875000-1876600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr5:1875000-1876600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:1875000-1876600	Enhancers	Pancreas	Pancrea
38	chr5:1875000-1877200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell

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