Variant report

Variant	rs1320628
Chromosome Location	chr11:64175986-64175987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10897491	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10897504	0.91[CEU][hapmap];0.91[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11231787	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11231789	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11601686	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11603861	0.82[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11605289	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12365369	0.85[ASN][1000 genomes]
rs12791477	0.86[ASN][1000 genomes]
rs488909	0.82[EUR][1000 genomes]
rs4930168	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4930175	0.82[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4963222	0.91[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4963223	0.91[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs506594	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs508326	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs570024	0.81[CEU][hapmap]
rs596308	0.81[MEX][hapmap]
rs7127926	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72927984	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs750830	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs750832	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7933523	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832187	chr11:64121969-64312300	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1320628	RNASEH2C	cis	parietal	SCAN
rs1320628	ESRRA	cis	cerebellum	SCAN
rs1320628	CCDC88B	cis	lymphoblastoid	seeQTL
rs1320628	TUT1	cis	parietal	SCAN
rs1320628	MS4A6E	cis	parietal	SCAN
rs1320628	TRPT1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64172600-64176000	Enhancers	Placenta	Placenta
2	chr11:64173000-64176000	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr11:64173000-64178800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr11:64173200-64178800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:64174200-64176600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:64174200-64177200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:64174200-64182200	Weak transcription	Spleen	Spleen
8	chr11:64174400-64176400	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:64174400-64176600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:64174400-64177400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:64174400-64177400	Weak transcription	Fetal Lung	lung
12	chr11:64174400-64177600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:64174400-64177600	Weak transcription	HSMMtube	muscle
14	chr11:64174400-64182400	Weak transcription	Right Ventricle	heart
15	chr11:64174400-64182600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:64174400-64182600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:64175000-64176800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr11:64175200-64176400	Weak transcription	Fetal Intestine Large	intestine
19	chr11:64175200-64176400	Weak transcription	Fetal Muscle Leg	muscle
20	chr11:64175200-64177400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:64175400-64176000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:64175400-64176600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:64175400-64177200	Weak transcription	Fetal Brain Male	brain
24	chr11:64175400-64177600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:64175600-64176600	Weak transcription	Fetal Stomach	stomach
26	chr11:64175600-64177000	Weak transcription	Fetal Heart	heart
27	chr11:64175600-64177000	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr11:64175600-64177400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:64175600-64177400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:64175600-64177800	Weak transcription	Fetal Intestine Small	intestine
31	chr11:64175600-64178200	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links