Variant report

Variant	rs10519348
Chromosome Location	chr5:112601878-112601879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112597661..112600348-chr5:112601306..112603277,2	MCF-7	breast:
2	chr5:112543815..112546269-chr5:112600639..112603401,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10519354	1.00[CHB][hapmap]
rs11739509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11740807	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11741176	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11750752	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13162970	1.00[JPT][hapmap]
rs13177178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13182359	1.00[JPT][hapmap]
rs1318772	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13188803	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13189851	0.83[ASN][1000 genomes]
rs164252	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17135605	1.00[MEX][hapmap]
rs17324474	0.83[ASN][1000 genomes]
rs17325908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17326496	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17327139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2120348	1.00[CHB][hapmap]
rs255857	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26965	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26980	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26982	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26984	1.00[JPT][hapmap]
rs26989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26990	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs34441430	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34614757	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34766128	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35352601	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36120874	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36611	1.00[JPT][hapmap]
rs36613	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs446272	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs458055	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs569540	1.00[MEX][hapmap]
rs66957398	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67894881	0.91[ASN][1000 genomes]
rs6861939	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72788641	0.91[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	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10519348	YTHDC2	cis	cerebellum	SCAN
rs10519348	DCP2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112583000-112604600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:112586600-112623600	Weak transcription	Pancreas	Pancrea
3	chr5:112587600-112617000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:112589200-112610600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:112589400-112602200	Weak transcription	Esophagus	oesophagus
6	chr5:112591600-112602000	Weak transcription	Brain Substantia Nigra	brain
7	chr5:112594400-112602200	Weak transcription	Left Ventricle	heart
8	chr5:112594400-112602200	Weak transcription	Right Ventricle	heart
9	chr5:112595600-112602200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:112598800-112603800	Enhancers	Liver	Liver
11	chr5:112599400-112603000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr5:112599800-112602000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:112599800-112602200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:112599800-112604800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:112600000-112602000	Weak transcription	Adipose Nuclei	Adipose
16	chr5:112600200-112602000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:112600200-112604800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:112600200-112605000	Weak transcription	NH-A	brain
19	chr5:112600200-112618000	Weak transcription	Fetal Kidney	kidney
20	chr5:112600400-112605200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:112600600-112602400	Enhancers	H9 Cell Line	embryonic stem cell
22	chr5:112600800-112602800	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr5:112600800-112602800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr5:112600800-112605000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr5:112600800-112607200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr5:112600800-112607600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr5:112600800-112608000	Enhancers	Ovary	ovary
28	chr5:112600800-112610600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:112600800-112610800	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr5:112601000-112602600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:112601000-112603400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr5:112601000-112604000	Enhancers	Fetal Heart	heart
33	chr5:112601000-112606200	Enhancers	Right Atrium	heart
34	chr5:112601000-112612400	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr5:112601200-112602400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:112601200-112602400	Enhancers	HMEC	breast
37	chr5:112601200-112603800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr5:112601200-112605000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:112601200-112605800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:112601400-112602200	Enhancers	Brain Hippocampus Middle	brain
41	chr5:112601400-112602200	Weak transcription	Placenta	Placenta
42	chr5:112601400-112602200	Enhancers	NHEK	skin
43	chr5:112601400-112611200	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr5:112601600-112602000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr5:112601600-112602000	Weak transcription	Fetal Lung	lung
46	chr5:112601800-112602600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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