Variant report

Variant	rs13187145
Chromosome Location	chr5:53240729-53240730
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10040674	0.85[ASN][1000 genomes]
rs13170364	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs16881847	0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs16881895	0.81[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs17251005	0.88[CHB][hapmap]
rs1838724	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816974	0.87[ASN][1000 genomes]
rs56016819	0.96[ASN][1000 genomes]
rs58614496	0.92[ASN][1000 genomes]
rs60633530	0.83[ASN][1000 genomes]
rs66505436	0.96[ASN][1000 genomes]
rs68101674	0.96[ASN][1000 genomes]
rs713209	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7726524	0.88[CHB][hapmap];0.87[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	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv533778	chr5:53092696-53284566	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv830299	chr5:53207020-53386600	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv880272	chr5:53213945-53277266	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13187145	CCDC24	trans	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53200800-53251600	Weak transcription	Primary B cells from cord blood	blood
2	chr5:53217200-53244800	Weak transcription	Pancreas	Pancrea
3	chr5:53220600-53251600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:53226800-53251200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:53230400-53241200	Weak transcription	Fetal Brain Male	brain
6	chr5:53231000-53244600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr5:53231200-53242600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:53231200-53242600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:53232600-53251400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:53233000-53240800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:53233000-53241000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:53233000-53252400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:53233400-53240800	Weak transcription	NHDF-Ad	bronchial
14	chr5:53233800-53240800	Weak transcription	Fetal Stomach	stomach
15	chr5:53233800-53251200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:53235600-53243400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:53235600-53251400	Weak transcription	Fetal Intestine Small	intestine
18	chr5:53237800-53240800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:53237800-53240800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:53237800-53241000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:53237800-53248200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:53237800-53253200	Weak transcription	Aorta	Aorta
23	chr5:53238000-53241200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:53238000-53242400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:53238400-53240800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr5:53238600-53241000	Strong transcription	Primary T cells from cord blood	blood
27	chr5:53238600-53241400	Enhancers	HUVEC	blood vessel
28	chr5:53239000-53242600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:53239000-53251600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:53239000-53271000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:53239400-53242000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:53239600-53251800	Weak transcription	Fetal Intestine Large	intestine
33	chr5:53239800-53240800	Weak transcription	K562	blood
34	chr5:53240200-53242200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:53240400-53241200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:53240600-53240800	Enhancers	HepG2	liver
37	chr5:53240600-53241400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:53240600-53241400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr5:53240600-53241400	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr5:53240600-53241800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr5:53240600-53242200	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr5:53240600-53252800	Weak transcription	Rectal Mucosa Donor 29	rectum

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