Variant report

Variant	rs16962974
Chromosome Location	chr18:29867091-29867092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10502593	1.00[CEU][hapmap]
rs10502597	1.00[CEU][hapmap]
rs10502598	1.00[CEU][hapmap]
rs10502599	1.00[CEU][hapmap]
rs11660076	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11661174	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11661186	0.93[EUR][1000 genomes]
rs11661378	1.00[CEU][hapmap]
rs11664951	1.00[CEU][hapmap]
rs11665544	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11873828	1.00[CEU][hapmap]
rs11877881	1.00[CEU][hapmap]
rs12052010	1.00[CEU][hapmap]
rs1380086	1.00[CEU][hapmap]
rs16962918	0.96[EUR][1000 genomes]
rs16962924	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16962941	1.00[CEU][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962953	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[EUR][1000 genomes]
rs16962965	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962977	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16963129	1.00[CEU][hapmap]
rs16963184	1.00[CEU][hapmap]
rs17743799	1.00[CEU][hapmap]
rs17743907	1.00[CEU][hapmap]
rs17744164	1.00[CEU][hapmap]
rs17805881	1.00[CEU][hapmap]
rs17805905	1.00[CEU][hapmap]
rs17805953	1.00[CEU][hapmap]
rs17811420	1.00[CEU][hapmap]
rs17811474	1.00[CEU][hapmap]
rs17811780	1.00[CEU][hapmap]
rs28482447	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3859366	1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[EUR][1000 genomes]
rs41535045	1.00[CEU][hapmap]
rs4462681	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60291556	0.96[EUR][1000 genomes]
rs60694040	0.82[EUR][1000 genomes]
rs7243861	0.93[EUR][1000 genomes]
rs7243963	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs73419859	0.96[EUR][1000 genomes]
rs8086611	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8086990	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8087394	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9916917	0.93[EUR][1000 genomes]
rs9947150	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9950965	0.90[EUR][1000 genomes]
rs9953127	1.00[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9960751	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9962307	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[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	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv833616	chr18:29792336-29964212	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv528846	chr18:29832147-29890042	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16962974	DSG2	cis	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29837400-29867200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:29839800-29871800	Weak transcription	HSMMtube	muscle
3	chr18:29848600-29867200	Weak transcription	Lung	lung
4	chr18:29850000-29877600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr18:29850400-29867200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr18:29858600-29877600	Weak transcription	Fetal Kidney	kidney
7	chr18:29859000-29867600	Weak transcription	Colonic Mucosa	Colon
8	chr18:29859000-29870400	Weak transcription	HepG2	liver
9	chr18:29859400-29867200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr18:29861000-29867200	Weak transcription	Gastric	stomach
11	chr18:29861000-29867400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr18:29861000-29871000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr18:29861000-29876000	Weak transcription	Small Intestine	intestine
14	chr18:29861600-29869400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr18:29861600-29869800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr18:29861600-29876800	Weak transcription	Stomach Mucosa	stomach
17	chr18:29862400-29872400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr18:29862600-29867600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr18:29863000-29869200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr18:29863200-29873000	Weak transcription	Right Ventricle	heart
21	chr18:29863200-29877000	Weak transcription	Fetal Heart	heart
22	chr18:29864000-29868200	Weak transcription	Psoas Muscle	Psoas
23	chr18:29864400-29869400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr18:29864400-29869800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr18:29864400-29870400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr18:29864400-29880800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr18:29864600-29881200	Weak transcription	Colon Smooth Muscle	Colon
28	chr18:29865000-29867400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr18:29865000-29868000	Strong transcription	Fetal Intestine Small	intestine
30	chr18:29865000-29868000	Strong transcription	Fetal Stomach	stomach
31	chr18:29865000-29868000	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr18:29865200-29868000	Strong transcription	Liver	Liver
33	chr18:29865200-29868000	Strong transcription	Brain Hippocampus Middle	brain
34	chr18:29865200-29868200	Strong transcription	Stomach Smooth Muscle	stomach
35	chr18:29865400-29867200	Weak transcription	Brain Germinal Matrix	brain
36	chr18:29865400-29867800	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr18:29865400-29867800	Strong transcription	Pancreas	Pancrea
38	chr18:29865400-29868000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr18:29865400-29868600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr18:29865600-29873200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr18:29865800-29868200	Strong transcription	Fetal Intestine Large	intestine
42	chr18:29865800-29868200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr18:29866200-29868000	Strong transcription	Ovary	ovary
44	chr18:29866200-29869200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr18:29866400-29867400	Active TSS	Aorta	Aorta
46	chr18:29866400-29868200	Strong transcription	Fetal Muscle Leg	muscle
47	chr18:29866600-29867800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr18:29866600-29867800	Strong transcription	Fetal Lung	lung
49	chr18:29866600-29868000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr18:29866600-29868000	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links