Variant report

Variant	rs1017238
Chromosome Location	chr16:81716546-81716547
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11647444	0.83[GIH][hapmap]
rs16955751	0.82[CEU][hapmap]
rs2012502	0.81[CHB][hapmap]
rs2288011	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28375552	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28437192	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4888163	0.84[ASN][1000 genomes]
rs4888164	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
2	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
3	nsv907011	chr16:81639190-81757252	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1017238	CDH13	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81682400-81722400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr16:81683800-81721800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:81684400-81722200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr16:81684400-81722200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr16:81686600-81721600	Weak transcription	NH-A	brain
6	chr16:81686600-81725000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr16:81688400-81736800	Weak transcription	NHDF-Ad	bronchial
8	chr16:81689800-81722200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr16:81689800-81722400	Strong transcription	Fetal Intestine Large	intestine
10	chr16:81691200-81721200	Strong transcription	Liver	Liver
11	chr16:81695200-81717000	Strong transcription	NHEK	skin
12	chr16:81698800-81721400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr16:81699200-81725600	Weak transcription	Osteobl	bone
14	chr16:81699400-81726000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr16:81701000-81725200	Weak transcription	Aorta	Aorta
16	chr16:81701200-81722200	Strong transcription	Fetal Intestine Small	intestine
17	chr16:81702200-81721800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr16:81702200-81722200	Strong transcription	HepG2	liver
19	chr16:81702600-81721600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:81703200-81722200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr16:81703400-81719000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr16:81703800-81717000	Strong transcription	Fetal Thymus	thymus
23	chr16:81703800-81717200	Strong transcription	Thymus	Thymus
24	chr16:81704200-81724600	Weak transcription	Hela-S3	cervix
25	chr16:81706600-81725200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr16:81708000-81721200	Weak transcription	GM12878-XiMat	blood
27	chr16:81709200-81716800	Strong transcription	Primary hematopoietic stem cells	blood
28	chr16:81709200-81716800	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr16:81709200-81717400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr16:81711000-81717000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr16:81712200-81716800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr16:81713000-81718000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr16:81713200-81716800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr16:81713200-81717000	Strong transcription	Spleen	Spleen
35	chr16:81713200-81719600	Weak transcription	Fetal Heart	heart
36	chr16:81713200-81721000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr16:81713200-81721400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr16:81713200-81721400	Weak transcription	K562	blood
39	chr16:81713200-81721600	Weak transcription	HSMM	muscle
40	chr16:81713200-81721600	Weak transcription	HSMMtube	muscle
41	chr16:81713200-81722400	Strong transcription	A549	lung
42	chr16:81713200-81724800	Weak transcription	Stomach Mucosa	stomach
43	chr16:81713200-81725200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr16:81713200-81726000	Weak transcription	Fetal Brain Male	brain
45	chr16:81713200-81726200	Weak transcription	Small Intestine	intestine
46	chr16:81713200-81727200	Weak transcription	NHLF	lung
47	chr16:81713200-81740600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr16:81713200-81744400	Weak transcription	Fetal Kidney	kidney
49	chr16:81713400-81717000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr16:81713400-81717800	Weak transcription	HUVEC	blood vessel

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