Variant report

Variant	rs672873
Chromosome Location	chr15:40395403-40395404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40376791..40380091-chr15:40393802..40397569,3	MCF-7	breast:
2	chr15:40361459..40366979-chr15:40389781..40395512,5	MCF-7	breast:
3	chr15:40343717..40348357-chr15:40394391..40397717,7	MCF-7	breast:
4	chr15:40345188..40347486-chr15:40391657..40395509,4	MCF-7	breast:
5	chr15:40339870..40341521-chr15:40394237..40395838,2	MCF-7	breast:
6	chr15:40328572..40331875-chr15:40394053..40397065,4	MCF-7	breast:
7	chr15:40395137..40397237-chr15:40456006..40457830,2	K562	blood:
8	chr15:40384981..40385891-chr15:40394864..40395872,3	MCF-7	breast:
9	chr15:40329348..40332922-chr15:40394377..40398986,5	MCF-7	breast:
10	chr15:40394940..40397179-chr15:40397500..40400223,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000248508	Chromatin interaction
ENSG00000140319	Chromatin interaction
ENSG00000104081	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10152521	0.81[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs488318	0.93[EUR][1000 genomes]
rs568800	0.81[MEX][hapmap];0.80[EUR][1000 genomes]
rs6492929	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178233	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs672873	LTBP1	trans	brain	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40387200-40395600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr15:40387200-40397800	Enhancers	Fetal Muscle Leg	muscle
3	chr15:40387600-40397200	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr15:40389200-40400000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:40389800-40400400	Enhancers	Small Intestine	intestine
6	chr15:40390400-40399800	Transcr. at gene 5' and 3'	Thymus	Thymus
7	chr15:40391000-40399800	Enhancers	Liver	Liver
8	chr15:40391200-40398800	Enhancers	Placenta	Placenta
9	chr15:40391400-40396600	Genic enhancers	Fetal Thymus	thymus
10	chr15:40391400-40396800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr15:40391400-40397600	Enhancers	NH-A	brain
12	chr15:40391400-40400000	Enhancers	Stomach Mucosa	stomach
13	chr15:40392000-40400000	Enhancers	Right Atrium	heart
14	chr15:40392000-40400000	Enhancers	Right Ventricle	heart
15	chr15:40392000-40400400	Enhancers	Pancreas	Pancrea
16	chr15:40392200-40400200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:40392400-40395800	Genic enhancers	Fetal Intestine Small	intestine
18	chr15:40392400-40397200	Genic enhancers	Primary B cells from peripheral blood	blood
19	chr15:40392400-40397600	Enhancers	Psoas Muscle	Psoas
20	chr15:40392400-40398400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:40392600-40396600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:40392600-40398600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:40392800-40397800	Enhancers	Lung	lung
24	chr15:40393400-40396800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:40393600-40396000	Enhancers	Primary B cells from cord blood	blood
26	chr15:40393600-40396400	Weak transcription	A549	lung
27	chr15:40393600-40396800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:40393800-40399200	Enhancers	Ovary	ovary
29	chr15:40393800-40400200	Enhancers	Esophagus	oesophagus
30	chr15:40394000-40396600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr15:40394000-40396800	Weak transcription	Dnd41	blood
32	chr15:40394000-40397600	Enhancers	Brain Angular Gyrus	brain
33	chr15:40394000-40400200	Enhancers	Left Ventricle	heart
34	chr15:40394200-40396400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr15:40394200-40396400	Weak transcription	HepG2	liver
36	chr15:40394200-40396600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:40394200-40396600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:40394200-40396600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr15:40394200-40396600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr15:40394200-40396800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:40394200-40396800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr15:40394200-40396800	Genic enhancers	Spleen	Spleen
43	chr15:40394200-40397200	Genic enhancers	Primary monocytes fromperipheralblood	blood
44	chr15:40394200-40397400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr15:40394200-40398400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:40394200-40398800	Enhancers	Gastric	stomach
47	chr15:40394200-40400000	Enhancers	Fetal Intestine Large	intestine
48	chr15:40394200-40400000	Enhancers	Fetal Muscle Trunk	muscle
49	chr15:40394400-40396400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:40394400-40396800	Weak transcription	Primary T cells from cord blood	blood

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