Variant report

Variant	rs2561547
Chromosome Location	chr19:41180687-41180688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41167496..41181822-chr19:41192475..41200102,20	MCF-7	breast:
2	chr19:41173668..41175905-chr19:41178921..41181635,2	K562	blood:
3	chr19:41167287..41169951-chr19:41180209..41183939,4	K562	blood:

Variant related genes	Relation type
ENSG00000105245	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10411347	0.88[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2250994	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2305797	1.00[LWK][hapmap]
rs2561539	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2561542	0.86[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2561543	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2561546	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2561548	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2561551	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2561555	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2604860	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2604879	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs2604892	0.88[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2604900	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4278858	0.90[EUR][1000 genomes]
rs8110611	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs890934	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv2489	chr19:41145034-41182170	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2561547	IRF2BP1	cis	parietal	SCAN
rs2561547	APOC4	cis	cerebellum	SCAN
rs2561547	KCNN4	cis	cerebellum	SCAN
rs2561547	C19orf54	Cis_1M	lymphoblastoid	RTeQTL
rs2561547	SULT2B1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41169800-41184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr19:41169800-41195400	Weak transcription	Psoas Muscle	Psoas
3	chr19:41170000-41180800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:41172000-41193000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr19:41172400-41191000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr19:41172600-41193400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:41172600-41193600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr19:41172800-41180800	Strong transcription	Colonic Mucosa	Colon
9	chr19:41172800-41191000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr19:41172800-41192000	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr19:41172800-41192800	Strong transcription	Adipose Nuclei	Adipose
12	chr19:41172800-41193200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:41172800-41193200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:41173000-41183000	Weak transcription	Stomach Mucosa	stomach
15	chr19:41173000-41184000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr19:41173000-41185200	Strong transcription	Aorta	Aorta
17	chr19:41173000-41192800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:41173000-41192800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:41173000-41192800	Strong transcription	Ovary	ovary
20	chr19:41173000-41193200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:41173000-41193200	Strong transcription	Osteobl	bone
22	chr19:41173200-41180800	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:41173200-41187200	Strong transcription	Fetal Intestine Large	intestine
24	chr19:41173200-41189800	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr19:41173200-41192600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr19:41173200-41192800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:41173200-41193200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:41173600-41180800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr19:41173600-41185400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:41173800-41180800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr19:41173800-41189600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:41174000-41180800	Strong transcription	HSMMtube	muscle
33	chr19:41174000-41185600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr19:41174000-41187400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:41174000-41189600	Strong transcription	HSMM	muscle
36	chr19:41174200-41193200	Strong transcription	Colon Smooth Muscle	Colon
37	chr19:41174400-41185200	Strong transcription	Brain Angular Gyrus	brain
38	chr19:41174600-41180800	Strong transcription	Rectal Smooth Muscle	rectum
39	chr19:41174800-41180800	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr19:41174800-41180800	Strong transcription	NHDF-Ad	bronchial
41	chr19:41174800-41184600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr19:41174800-41190000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr19:41175600-41184200	Strong transcription	Brain Substantia Nigra	brain
44	chr19:41175800-41181000	Strong transcription	Brain Hippocampus Middle	brain
45	chr19:41175800-41181400	Strong transcription	Brain Cingulate Gyrus	brain
46	chr19:41175800-41184000	Strong transcription	HUVEC	blood vessel
47	chr19:41175800-41184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:41175800-41184600	Strong transcription	Fetal Lung	lung
49	chr19:41175800-41185000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:41175800-41187400	Strong transcription	NH-A	brain

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