Variant report

Variant	rs4625625
Chromosome Location	chr13:52300847-52300848
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52300204..52302832-chr13:52303921..52305515,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1024271	0.95[JPT][hapmap]
rs12585249	0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs17075881	1.00[YRI][hapmap]
rs17075900	1.00[YRI][hapmap]
rs17075902	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4075628	0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs4941703	0.85[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs4941710	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4943005	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs4943009	0.80[CHD][hapmap];0.89[GIH][hapmap]
rs4943018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7328589	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7328695	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7332603	1.00[YRI][hapmap]
rs7332922	0.82[YRI][hapmap]
rs7333623	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs745374	0.85[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs7986066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7993522	1.00[YRI][hapmap]
rs9316547	0.90[JPT][hapmap]
rs9316551	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs9563063	0.85[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs9563065	0.87[ASN][1000 genomes]
rs9563066	0.87[ASN][1000 genomes]
rs9563067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568644	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9568647	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568649	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568650	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568658	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9805172	0.85[CHB][hapmap];0.95[JPT][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	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4625625	TRIM13	cis	cerebellum	SCAN
rs4625625	WDFY2	cis	parietal	SCAN
rs4625625	NCRNA00282	cis	parietal	SCAN
rs4625625	MANF	trans	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52249400-52307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:52254600-52301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:52270800-52301600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr13:52271200-52301800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr13:52276600-52301800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:52278800-52301800	Weak transcription	Thymus	Thymus
7	chr13:52278800-52302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr13:52279400-52301800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:52279400-52301800	Weak transcription	Gastric	stomach
10	chr13:52279400-52303000	Weak transcription	Lung	lung
11	chr13:52279600-52301800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr13:52279600-52301800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr13:52279600-52304000	Weak transcription	Esophagus	oesophagus
14	chr13:52280200-52301600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr13:52282000-52302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr13:52284800-52301000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr13:52288400-52322200	Weak transcription	K562	blood
18	chr13:52288600-52303000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr13:52289000-52301800	Weak transcription	A549	lung
20	chr13:52289400-52305800	Weak transcription	Fetal Kidney	kidney
21	chr13:52290000-52307600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr13:52290200-52301600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:52291400-52303000	Weak transcription	Fetal Stomach	stomach
24	chr13:52292200-52301800	Weak transcription	Dnd41	blood
25	chr13:52292200-52302600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr13:52292200-52304400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr13:52292400-52304400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr13:52293200-52303200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:52293600-52301800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr13:52293600-52307600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr13:52294200-52304400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr13:52294600-52302800	Weak transcription	HMEC	breast
33	chr13:52295600-52304600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr13:52295800-52301800	Weak transcription	HSMMtube	muscle
35	chr13:52296000-52301800	Weak transcription	Left Ventricle	heart
36	chr13:52296000-52301800	Weak transcription	Pancreas	Pancrea
37	chr13:52296000-52301800	Weak transcription	Right Atrium	heart
38	chr13:52296000-52303000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr13:52296000-52303000	Weak transcription	Fetal Muscle Leg	muscle
40	chr13:52296000-52303000	Weak transcription	Spleen	Spleen
41	chr13:52296000-52304400	Weak transcription	Right Ventricle	heart
42	chr13:52296000-52304400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr13:52296000-52307600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr13:52296200-52303000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr13:52296200-52303000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr13:52296200-52303600	Weak transcription	Aorta	Aorta
47	chr13:52296200-52303600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr13:52296400-52303200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr13:52296400-52322200	Weak transcription	Fetal Heart	heart
50	chr13:52297000-52311800	Weak transcription	GM12878-XiMat	blood

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