Variant report

Variant	rs1871417
Chromosome Location	chr12:58018979-58018980
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58007372..58011848-chr12:58013286..58019253,6	MCF-7	breast:
2	chr12:58018186..58020875-chr12:58113859..58115520,2	K562	blood:
3	chr12:57912625..57916215-chr12:58016074..58021603,6	K562	blood:

Variant related genes	Relation type
ENSG00000175197	Chromatin interaction
ENSG00000224713	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000257342	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10082911	0.88[EUR][1000 genomes]
rs10083154	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783836	0.86[EUR][1000 genomes]
rs10783842	0.83[EUR][1000 genomes]
rs10783844	0.88[EUR][1000 genomes]
rs1082502	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1082503	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876993	0.92[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs10877001	0.92[CEU][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs10877006	0.88[EUR][1000 genomes]
rs10877007	0.87[EUR][1000 genomes]
rs10877008	0.89[EUR][1000 genomes]
rs1092472	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172277	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11172306	0.88[EUR][1000 genomes]
rs12302351	0.83[EUR][1000 genomes]
rs12302451	0.85[EUR][1000 genomes]
rs12314562	0.90[EUR][1000 genomes]
rs12316021	0.83[EUR][1000 genomes]
rs12809742	0.85[EUR][1000 genomes]
rs1585781	0.90[EUR][1000 genomes]
rs1628552	0.91[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs1629032	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678504	0.87[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1678505	0.82[EUR][1000 genomes]
rs1678511	0.90[EUR][1000 genomes]
rs1678512	0.91[EUR][1000 genomes]
rs1678513	0.91[EUR][1000 genomes]
rs1678515	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678516	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678519	0.83[ASN][1000 genomes]
rs1678520	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678522	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1678527	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678529	0.89[EUR][1000 genomes]
rs1678530	0.90[EUR][1000 genomes]
rs1678531	0.90[EUR][1000 genomes]
rs1678532	0.90[EUR][1000 genomes]
rs1678534	0.89[EUR][1000 genomes]
rs1678539	0.90[EUR][1000 genomes]
rs1678540	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs1689584	0.89[EUR][1000 genomes]
rs1689585	0.92[CEU][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs1689586	0.88[EUR][1000 genomes]
rs1689592	0.91[EUR][1000 genomes]
rs1689594	0.91[EUR][1000 genomes]
rs1689595	0.92[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1689596	0.90[EUR][1000 genomes]
rs1689597	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1689600	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1689601	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1689604	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2169987	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277322	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2619441	0.88[EUR][1000 genomes]
rs2619466	0.90[EUR][1000 genomes]
rs2640629	0.92[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap]
rs2640630	0.89[EUR][1000 genomes]
rs2640631	0.92[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs2928053	0.89[EUR][1000 genomes]
rs2928054	0.83[EUR][1000 genomes]
rs2928055	0.85[EUR][1000 genomes]
rs2928061	0.89[EUR][1000 genomes]
rs2928062	0.82[EUR][1000 genomes]
rs2928064	0.82[EUR][1000 genomes]
rs3825078	0.87[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs4760164	0.88[EUR][1000 genomes]
rs4760165	0.89[EUR][1000 genomes]
rs4760168	0.87[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs701006	0.82[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs703832	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7136269	0.90[EUR][1000 genomes]
rs7314152	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774887	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774888	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774890	0.92[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap]
rs774891	0.89[EUR][1000 genomes]
rs7976852	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs7979246	0.83[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs799575	0.90[EUR][1000 genomes]
rs810204	0.89[EUR][1000 genomes]

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	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS 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 miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1871417	FAM119B	cis	lymphoblastoid	seeQTL
rs1871417	CDK4	cis	cerebellum	SCAN
rs1871417	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs1871417	ITGB7	cis	cerebellum	SCAN
rs1871417	KRT75	cis	cerebellum	SCAN
rs1871417	DKFZP586D0919	cis	multi-tissue	Pritchard
rs1871417	SLC26A10	cis	multi-tissue	Pritchard
rs1871417	CDK2	cis	parietal	SCAN
rs1871417	HSD17B6	cis	cerebellum	SCAN
rs1871417	SLC26A10	cis	Heart Left Ventricle	GTEx
rs1871417	TSPAN31	cis	parietal	SCAN
rs1871417	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1871417	FAM119B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58012000-58019000	Weak transcription	Aorta	Aorta
2	chr12:58015600-58021400	Weak transcription	Gastric	stomach
3	chr12:58016000-58019600	Weak transcription	A549	lung
4	chr12:58016000-58020000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:58016000-58021200	Weak transcription	Pancreas	Pancrea
6	chr12:58016200-58020000	Weak transcription	Spleen	Spleen
7	chr12:58016200-58021400	Weak transcription	Right Ventricle	heart
8	chr12:58017000-58025000	Weak transcription	K562	blood
9	chr12:58018000-58019200	Weak transcription	Fetal Brain Female	brain
10	chr12:58018000-58024600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:58018600-58023000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:58018800-58019200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr12:58018800-58021600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:58018800-58024000	Strong transcription	Brain Germinal Matrix	brain
15	chr12:58018800-58024200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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