Variant report

Variant	rs12459611
Chromosome Location	chr19:35690539-35690540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:35690432..35694282-chr19:35737406..35740998,3	K562	blood:
2	chr19:35688853..35690621-chr19:35737302..35739922,2	MCF-7	breast:
3	chr19:35688259..35691483-chr19:35738721..35741363,4	MCF-7	breast:
4	chr19:35689192..35690781-chr19:35710324..35712969,2	K562	blood:
5	chr19:35689748..35692688-chr19:35698548..35701014,3	K562	blood:

Variant related genes	Relation type
ENSG00000105699	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12978479	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12984052	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2106447	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34197953	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34571941	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3458	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35436785	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35575880	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36087337	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71352910	0.87[AMR][1000 genomes];0.88[EUR][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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv2470	chr19:35655281-35702565	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12459611	FXYD5	cis	Skin Sun Exposed Lower leg	GTEx
rs12459611	FXYD5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35685400-35691800	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr19:35685600-35693800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:35685800-35691800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr19:35688000-35692000	Weak transcription	K562	blood
5	chr19:35689600-35690600	Enhancers	Primary T cells fromperipheralblood	blood
6	chr19:35689600-35691000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr19:35689800-35690600	Enhancers	H9 Cell Line	embryonic stem cell
8	chr19:35690000-35690600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr19:35690000-35690600	Enhancers	Spleen	Spleen
10	chr19:35690000-35690800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr19:35690000-35690800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr19:35690000-35691000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr19:35690000-35692200	Enhancers	Stomach Mucosa	stomach
14	chr19:35690000-35692400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:35690000-35693400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:35690200-35690600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr19:35690200-35690600	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr19:35690200-35690800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:35690200-35690800	Enhancers	Gastric	stomach
20	chr19:35690200-35693400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:35690400-35690600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr19:35690400-35691800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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