Variant report

Variant	rs750832
Chromosome Location	chr11:64163302-64163303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRMT112-2	chr11:64162677-64163303	XLOC_009463

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10897491	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10897504	0.91[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11231787	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11231789	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11601686	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11603861	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11605289	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12365369	0.89[ASN][1000 genomes]
rs12791477	0.85[ASN][1000 genomes]
rs1320628	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs474901	1.00[YRI][hapmap]
rs4930168	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4930175	0.82[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4963222	0.91[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4963223	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs506594	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs508326	0.93[EUR][1000 genomes]
rs519763	1.00[YRI][hapmap]
rs570024	0.81[CEU][hapmap]
rs574087	1.00[YRI][hapmap]
rs596308	0.81[MEX][hapmap]
rs600377	1.00[YRI][hapmap]
rs612448	1.00[YRI][hapmap]
rs694739	1.00[YRI][hapmap]
rs7127926	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72927984	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs750830	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7933523	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs915987	1.00[YRI][hapmap]

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	nsv832186	chr11:63972260-64170059	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer 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	180 gene(s)	inside rSNPs	diseases
2	nsv897682	chr11:63999529-64170500	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs750832	ESRRA	cis	cerebellum	SCAN
rs750832	MS4A6E	cis	parietal	SCAN
rs750832	TUT1	cis	parietal	SCAN
rs750832	TRPT1	cis	cerebellum	SCAN
rs750832	RNASEH2C	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64154000-64167600	Weak transcription	Right Atrium	heart
2	chr11:64161600-64164000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
3	chr11:64161600-64164200	Enhancers	Fetal Thymus	thymus
4	chr11:64161600-64164200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr11:64161800-64164800	Enhancers	Fetal Muscle Trunk	muscle
6	chr11:64162000-64163800	Enhancers	Liver	Liver
7	chr11:64162000-64163800	Enhancers	Thymus	Thymus
8	chr11:64162000-64164200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr11:64162000-64164200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr11:64162000-64164400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr11:64162000-64164400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:64162000-64164800	Enhancers	Fetal Muscle Leg	muscle
13	chr11:64162200-64163400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr11:64162200-64164200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr11:64162400-64164400	Enhancers	Fetal Stomach	stomach
16	chr11:64162600-64163400	Enhancers	Brain Substantia Nigra	brain
17	chr11:64162600-64163400	Enhancers	Colonic Mucosa	Colon
18	chr11:64162600-64163400	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr11:64162600-64164000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:64162600-64164200	Enhancers	Adipose Nuclei	Adipose
21	chr11:64162600-64164400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:64162600-64164400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:64162600-64164400	Enhancers	Placenta	Placenta
24	chr11:64162800-64163800	Enhancers	H9 Cell Line	embryonic stem cell
25	chr11:64162800-64164000	Enhancers	Fetal Intestine Small	intestine
26	chr11:64163000-64163400	Active TSS	Duodenum Mucosa	Duodenum
27	chr11:64163000-64163400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
28	chr11:64163000-64163400	Enhancers	HepG2	liver
29	chr11:64163000-64163800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr11:64163000-64163800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:64163000-64164000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr11:64163000-64164200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:64163000-64164200	Enhancers	Colon Smooth Muscle	Colon
34	chr11:64163000-64164200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr11:64163000-64164200	Enhancers	HSMMtube	muscle
36	chr11:64163000-64164400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:64163000-64164400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:64163000-64164400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:64163000-64164400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:64163000-64164400	Enhancers	Fetal Kidney	kidney
41	chr11:64163200-64163400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:64163200-64163400	Enhancers	HSMM	muscle
43	chr11:64163200-64163800	Enhancers	Primary B cells from cord blood	blood
44	chr11:64163200-64163800	Weak transcription	Fetal Intestine Large	intestine
45	chr11:64163200-64163800	Enhancers	Ovary	ovary
46	chr11:64163200-64163800	Enhancers	Right Ventricle	heart
47	chr11:64163200-64163800	Enhancers	Spleen	Spleen
48	chr11:64163200-64164000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr11:64163200-64164000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr11:64163200-64164000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links