Variant report

Variant	rs561667
Chromosome Location	chr11:64162684-64162685
allele	C/G
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: 21 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10792432	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10897503	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1662189	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2083711	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930353	0.82[CEU][hapmap]
rs521319	0.96[EUR][1000 genomes]
rs548333	0.95[CEU][hapmap];0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs562560	0.84[EUR][1000 genomes]
rs564163	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs566409	0.96[EUR][1000 genomes]
rs577304	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61884054	0.85[EUR][1000 genomes]
rs653565	0.81[GIH][hapmap]
rs653578	0.81[GIH][hapmap]
rs7936543	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7937023	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7937125	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951702	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs561667	ZBTB3	cis	parietal	SCAN
rs561667	POLD4	cis	cerebellum	SCAN
rs561667	PPP1CA	cis	parietal	SCAN
rs561667	SLC25A45	cis	parietal	SCAN
rs561667	TUBGCP2	trans	lymphoblastoid	seeQTL
rs561667	KDM2A	cis	parietal	SCAN
rs561667	FKBP2	cis	cerebellum	SCAN
rs561667	FKBP2	cis	parietal	SCAN
rs561667	TRMT112	cis	parietal	SCAN
rs561667	CCDC88B	cis	cerebellum	SCAN
rs561667	CCS	cis	cerebellum	SCAN
rs561667	CD6	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64150600-64163000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:64153800-64163200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:64154000-64167600	Weak transcription	Right Atrium	heart
4	chr11:64159200-64163200	Weak transcription	Primary B cells from cord blood	blood
5	chr11:64159400-64163000	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:64159400-64163200	Weak transcription	Right Ventricle	heart
7	chr11:64159600-64163000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:64159600-64163200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:64159600-64163200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:64159600-64163200	Weak transcription	Spleen	Spleen
11	chr11:64160400-64163000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:64160600-64163000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr11:64161600-64164000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr11:64161600-64164200	Enhancers	Fetal Thymus	thymus
15	chr11:64161600-64164200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr11:64161800-64164800	Enhancers	Fetal Muscle Trunk	muscle
17	chr11:64162000-64163800	Enhancers	Liver	Liver
18	chr11:64162000-64163800	Enhancers	Thymus	Thymus
19	chr11:64162000-64164200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr11:64162000-64164200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr11:64162000-64164400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr11:64162000-64164400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:64162000-64164800	Enhancers	Fetal Muscle Leg	muscle
24	chr11:64162200-64162800	Bivalent Enhancer	Fetal Intestine Small	intestine
25	chr11:64162200-64163200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr11:64162200-64163400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr11:64162200-64164200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr11:64162400-64162800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:64162400-64163000	Weak transcription	Fetal Intestine Large	intestine
30	chr11:64162400-64164400	Enhancers	Fetal Stomach	stomach
31	chr11:64162600-64162800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr11:64162600-64162800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
33	chr11:64162600-64163400	Enhancers	Brain Substantia Nigra	brain
34	chr11:64162600-64163400	Enhancers	Colonic Mucosa	Colon
35	chr11:64162600-64163400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr11:64162600-64164000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:64162600-64164200	Enhancers	Adipose Nuclei	Adipose
38	chr11:64162600-64164400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:64162600-64164400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:64162600-64164400	Enhancers	Placenta	Placenta

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