Variant report

Variant	rs11660777
Chromosome Location	chr18:29426669-29426670
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10468903	0.88[TSI][hapmap]
rs11081720	0.85[CEU][hapmap]
rs11081728	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11081729	0.85[CEU][hapmap]
rs11660557	0.85[CEU][hapmap]
rs11661525	0.83[CEU][hapmap]
rs11662697	0.85[CEU][hapmap]
rs12326860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12604691	0.85[CEU][hapmap]
rs12606962	0.84[CEU][hapmap]
rs12607786	0.85[CEU][hapmap]
rs17742014	0.85[CEU][hapmap]
rs17742105	0.85[CEU][hapmap]
rs17804129	0.85[CEU][hapmap]
rs1815821	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276144	0.85[CEU][hapmap]
rs2276145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4545895	0.85[CEU][hapmap]
rs56046214	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56260330	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62093865	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7228817	0.85[CEU][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	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
2	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
3	nsv431975	chr18:29311034-29527902	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1057229	chr18:29335175-29514265	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11660777	RBPMS	trans	lymphoblastoid	seeQTL
rs11660777	DSC1	cis	parietal	SCAN
rs11660777	FAM59A	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29405600-29481800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:29406200-29518600	Weak transcription	Fetal Brain Male	brain
3	chr18:29406800-29431600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr18:29407400-29427400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr18:29407400-29429800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr18:29407400-29432000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:29407800-29431200	Weak transcription	Psoas Muscle	Psoas
8	chr18:29408000-29460200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:29408600-29471800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr18:29409000-29439000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr18:29409000-29456600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr18:29409600-29430000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr18:29409600-29430600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr18:29409800-29432000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr18:29409800-29466600	Weak transcription	Gastric	stomach
16	chr18:29410400-29431400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr18:29413200-29437200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr18:29413800-29456600	Weak transcription	Spleen	Spleen
19	chr18:29414200-29444800	Strong transcription	Fetal Thymus	thymus
20	chr18:29414400-29448200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr18:29415800-29461800	Weak transcription	Fetal Heart	heart
22	chr18:29416000-29432000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr18:29416200-29430000	Weak transcription	Lung	lung
24	chr18:29416200-29456600	Weak transcription	Aorta	Aorta
25	chr18:29416600-29427800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr18:29417600-29515600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr18:29418200-29429800	Weak transcription	Fetal Intestine Small	intestine
28	chr18:29418200-29431400	Weak transcription	Fetal Stomach	stomach
29	chr18:29418400-29454800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr18:29418400-29470400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr18:29418600-29428000	Weak transcription	HMEC	breast
32	chr18:29418600-29431800	Weak transcription	Small Intestine	intestine
33	chr18:29418600-29432000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr18:29418600-29436000	Weak transcription	Pancreas	Pancrea
35	chr18:29418600-29454400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr18:29418600-29456600	Weak transcription	Right Ventricle	heart
37	chr18:29418800-29430400	Weak transcription	Fetal Kidney	kidney
38	chr18:29418800-29431000	Weak transcription	HSMMtube	muscle
39	chr18:29418800-29431400	Weak transcription	Brain Angular Gyrus	brain
40	chr18:29418800-29431400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr18:29418800-29431600	Weak transcription	Brain Substantia Nigra	brain
42	chr18:29418800-29431800	Weak transcription	Brain Anterior Caudate	brain
43	chr18:29418800-29432000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr18:29418800-29432000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr18:29418800-29454800	Weak transcription	Colonic Mucosa	Colon
46	chr18:29418800-29456600	Weak transcription	NHEK	skin
47	chr18:29419000-29429200	Weak transcription	K562	blood
48	chr18:29419000-29431400	Weak transcription	Colon Smooth Muscle	Colon
49	chr18:29419000-29431800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr18:29419000-29431800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links