Variant report

Variant	rs2414172
Chromosome Location	chr15:52968955-52968956
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50645577..50647649-chr15:52968775..52972037,3	MCF-7	breast:
2	chr15:52856629..52859409-chr15:52967140..52969725,2	K562	blood:
3	chr15:52859855..52863944-chr15:52968349..52971887,6	MCF-7	breast:
4	chr15:52580574..52582076-chr15:52967362..52969063,2	MCF-7	breast:
5	chr15:52967401..52973659-chr15:53000765..53004676,11	MCF-7	breast:
6	chr15:52968259..52973250-chr15:52997483..53005703,18	MCF-7	breast:
7	chr15:52855349..52864927-chr15:52966670..52972620,15	MCF-7	breast:
8	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000047346	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000128989	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17651844	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs17651850	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs17708373	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35689765	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751613	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57141956	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59336405	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59360599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59808396	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59920981	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59997215	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60200908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61021982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182896	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72623993	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72623994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72623995	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72623996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72623997	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72623998	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72623999	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72624000	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs877974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877975	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs933861	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2414172	Hs.11898	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52944400-52969600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:52944400-52970200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:52944600-52969800	Weak transcription	Fetal Brain Male	brain
4	chr15:52950400-52969400	Weak transcription	A549	lung
5	chr15:52951000-52970200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:52957400-52970000	Weak transcription	Colonic Mucosa	Colon
7	chr15:52957400-52970000	Weak transcription	Lung	lung
8	chr15:52960000-52969000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:52960400-52969600	Weak transcription	HMEC	breast
10	chr15:52960600-52969400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:52960600-52969400	Weak transcription	NHEK	skin
12	chr15:52960600-52970000	Weak transcription	Small Intestine	intestine
13	chr15:52961600-52969000	Strong transcription	Osteobl	bone
14	chr15:52962200-52969800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:52962400-52969400	Weak transcription	Fetal Stomach	stomach
16	chr15:52962600-52969800	Weak transcription	Right Ventricle	heart
17	chr15:52962600-52970200	Weak transcription	Gastric	stomach
18	chr15:52962600-52970400	Weak transcription	Spleen	Spleen
19	chr15:52962800-52969400	Weak transcription	Aorta	Aorta
20	chr15:52963000-52969600	Weak transcription	NHLF	lung
21	chr15:52963000-52970000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:52964000-52969000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:52964600-52969400	Weak transcription	Thymus	Thymus
24	chr15:52964600-52969800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:52964600-52970000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:52965000-52969000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
27	chr15:52965000-52969800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:52965200-52969000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr15:52965400-52969600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:52965400-52969800	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr15:52965800-52969000	Weak transcription	Fetal Brain Female	brain
32	chr15:52965800-52969600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:52965800-52969600	Weak transcription	HSMMtube	muscle
34	chr15:52966000-52969600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:52966200-52969400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:52966200-52969400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:52966200-52969600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:52966400-52969600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:52966400-52969800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr15:52966600-52969000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr15:52966600-52969000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:52966600-52969000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:52966600-52969400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:52967200-52969000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr15:52967200-52969600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr15:52967200-52969600	Enhancers	Colon Smooth Muscle	Colon
47	chr15:52967400-52972400	Active TSS	Right Atrium	heart
48	chr15:52967600-52969000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:52967600-52969000	Enhancers	Dnd41	blood
50	chr15:52967600-52969800	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links