Variant report

Variant	rs12589185
Chromosome Location	chr14:22180214-22180215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr14:22180079-22180658	SK-N-SH	brain:	n/a	chr14:22180472-22180481 chr14:22180407-22180416
2	CTCF	chr14:22179318-22180258	A549	lung:	n/a	chr14:22179774-22179795 chr14:22179773-22179789 chr14:22179772-22179790 chr14:22179775-22179788 chr14:22179775-22179788

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:22179693..22180223-chr14:22202227..22202999,2	MCF-7	breast:

Variant related genes	Relation type
TRAV2	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10132760	0.90[CEU][hapmap]
rs10141478	0.81[YRI][hapmap]
rs10148566	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10151114	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1018344	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1018345	0.90[CEU][hapmap]
rs12431503	0.85[JPT][hapmap]
rs12589513	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs12589962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17182761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997532	0.89[CEU][hapmap]
rs1997533	0.90[CEU][hapmap]
rs2319874	0.96[ASN][1000 genomes]
rs2319875	0.96[ASN][1000 genomes]
rs28575550	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap]
rs4513011	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4528483	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4628878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982486	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs4982487	0.95[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs55654479	0.96[ASN][1000 genomes]
rs6650488	0.85[JPT][hapmap]
rs7143695	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7148008	0.82[JPT][hapmap];0.84[YRI][hapmap]
rs7150049	0.90[CEU][hapmap]
rs7155323	0.81[EUR][1000 genomes]
rs7158141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003447	0.85[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap]
rs8011509	0.90[CEU][hapmap]
rs8011979	0.90[CEU][hapmap]
rs8013476	0.87[ASW][hapmap];0.95[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8016911	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8018604	0.90[CEU][hapmap]
rs8019537	0.85[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap]
rs8020038	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs8020165	0.89[CEU][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap]
rs8022088	0.88[CEU][hapmap]
rs8022425	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap]
rs9323020	0.81[TSI][hapmap];0.81[YRI][hapmap]

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	nsv1042309	chr14:22042511-22866936	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	90 gene(s)	inside rSNPs	diseases
2	nsv456147	chr14:22073473-22305071	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv563851	chr14:22073473-22305071	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv510629	chr14:22134425-22215842	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12589185	EDDM3B	cis	parietal	SCAN
rs12589185	THTPA	cis	cerebellum	SCAN
rs12589185	OR4K15	cis	cerebellum	SCAN
rs12589185	SLC39A2	cis	cerebellum	SCAN
rs12589185	OR4N2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:22172600-22180600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr14:22180200-22180400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
3	chr14:22180200-22180600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links