Variant report

Variant	rs2414130
Chromosome Location	chr15:52402476-52402477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52388531..52391551-chr15:52401411..52403881,3	MCF-7	breast:
2	chr15:52262677..52264406-chr15:52400501..52402601,2	MCF-7	breast:
3	chr15:52395553..52398772-chr15:52399645..52403144,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12438169	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs12438743	0.89[GIH][hapmap]
rs12438937	0.85[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs12440354	0.88[ASN][1000 genomes]
rs12440956	0.90[EUR][1000 genomes]
rs12441074	0.88[ASN][1000 genomes]
rs12593041	0.85[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs12899030	0.82[ASW][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12899343	0.81[ASW][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12901354	0.90[EUR][1000 genomes]
rs12902522	0.88[ASN][1000 genomes]
rs12905698	0.85[ASN][1000 genomes]
rs12909161	0.89[GIH][hapmap]
rs12909184	0.85[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs12910052	0.85[ASN][1000 genomes]
rs12910398	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12910870	0.82[ASN][1000 genomes]
rs12912428	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2227308	1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2231297	1.00[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2398	1.00[CEU][hapmap];0.93[GIH][hapmap];0.89[EUR][1000 genomes]
rs2414132	0.88[ASW][hapmap];0.93[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35709612	0.88[ASN][1000 genomes]
rs35733550	0.82[ASN][1000 genomes]
rs3794543	0.89[GIH][hapmap]
rs4238384	0.85[CHB][hapmap];0.84[CHD][hapmap];0.90[ASN][1000 genomes]
rs4506834	0.82[ASN][1000 genomes]
rs4638520	0.93[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4776003	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs4776007	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs4776008	0.82[ASN][1000 genomes]
rs62014721	0.89[ASN][1000 genomes]
rs62014722	0.90[ASN][1000 genomes]
rs7166799	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs7177248	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs8029782	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2414130	KIAA1370	cis	parietal	SCAN
rs2414130	FGF7	cis	cerebellum	SCAN
rs2414130	ARPP19	cis	parietal	SCAN
rs2414130	TMOD2	cis	parietal	SCAN
rs2414130	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52398600-52403600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:52398600-52404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:52399000-52404000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:52399400-52404000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:52400400-52402600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:52400800-52402800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:52401000-52402600	Flanking Active TSS	GM12878-XiMat	blood
8	chr15:52401000-52404200	Enhancers	Primary B cells from peripheral blood	blood
9	chr15:52401800-52403000	Enhancers	Primary B cells from cord blood	blood
10	chr15:52402200-52402600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr15:52402200-52404200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:52402200-52404200	Weak transcription	Pancreas	Pancrea
13	chr15:52402200-52411400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:52402400-52402600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:52402400-52405600	Weak transcription	HepG2	liver

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