Variant report

Variant	rs1551006
Chromosome Location	chr18:29233245-29233246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10775449	0.86[CHB][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs11081706	0.96[CEU][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12327203	0.83[ASW][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];1.00[MKK][hapmap]
rs12456085	0.82[AFR][1000 genomes]
rs12970031	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1449082	0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap]
rs1449085	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs1449087	0.85[ASW][hapmap];0.96[CEU][hapmap];0.83[GIH][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17661533	1.00[YRI][hapmap]
rs1979105	0.81[CHB][hapmap]
rs4799589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718780	0.83[ASW][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs968325	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831348	chr18:29205526-29268786	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1551006	DSC1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29202800-29235000	Weak transcription	Pancreas	Pancrea
2	chr18:29202800-29240200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr18:29204600-29238600	Weak transcription	Gastric	stomach
4	chr18:29219200-29240000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:29219200-29252000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr18:29219200-29252000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr18:29223200-29236400	Weak transcription	Esophagus	oesophagus
8	chr18:29225200-29233600	Weak transcription	Dnd41	blood
9	chr18:29227400-29238000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr18:29227600-29252000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr18:29227800-29238800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr18:29227800-29240800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr18:29228200-29236600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr18:29228600-29233800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr18:29228600-29235200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:29228600-29238000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr18:29229000-29233400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr18:29229200-29236800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr18:29229200-29238200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr18:29229200-29238200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr18:29229200-29245200	Weak transcription	Brain Anterior Caudate	brain
22	chr18:29229400-29234600	Weak transcription	HUVEC	blood vessel
23	chr18:29229400-29238600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr18:29229400-29239600	Weak transcription	Brain Hippocampus Middle	brain
25	chr18:29229400-29239600	Weak transcription	Right Atrium	heart
26	chr18:29229400-29252800	Weak transcription	NHEK	skin
27	chr18:29229600-29238200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr18:29229600-29239800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr18:29229800-29236800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr18:29230400-29233600	Weak transcription	Fetal Intestine Small	intestine
31	chr18:29230400-29236800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr18:29230600-29237400	Weak transcription	Fetal Intestine Large	intestine
33	chr18:29230600-29238200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr18:29230800-29235000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr18:29231000-29238200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr18:29231200-29242400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr18:29231600-29235000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr18:29231600-29235200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr18:29231800-29233400	Enhancers	Primary B cells from cord blood	blood
40	chr18:29231800-29251800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr18:29232000-29233400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr18:29232800-29234000	Enhancers	Primary hematopoietic stem cells	blood
43	chr18:29232800-29236200	Weak transcription	Thymus	Thymus
44	chr18:29233000-29233800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr18:29233000-29234000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr18:29233000-29239200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr18:29233200-29233600	Enhancers	GM12878-XiMat	blood
48	chr18:29233200-29234200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr18:29233200-29237800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr18:29233200-29238800	Weak transcription	Fetal Thymus	thymus

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