Variant report

Variant	rs12354914
Chromosome Location	chr10:991208-991209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:987204..991340-chr10:993290..996064,4	MCF-7	breast:
2	chr10:989792..992480-chr10:1084980..1087131,2	MCF-7	breast:
3	chr10:989315..991705-chr10:1095222..1096768,2	MCF-7	breast:
4	chr10:983720..986820-chr10:989199..992227,3	MCF-7	breast:
5	chr10:991162..993286-chr10:1002150..1004961,2	K562	blood:
6	chr10:990098..992111-chr10:1033029..1035814,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205740	Chromatin interaction
ENSG00000107937	Chromatin interaction
ENSG00000047056	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1013504	1.00[ASN][1000 genomes]
rs10903358	1.00[ASN][1000 genomes]
rs10904564	1.00[ASN][1000 genomes]
rs10904565	1.00[ASN][1000 genomes]
rs10904566	1.00[ASN][1000 genomes]
rs11253414	1.00[ASN][1000 genomes]
rs11253419	1.00[ASN][1000 genomes]
rs11253420	1.00[ASN][1000 genomes]
rs11253421	1.00[ASN][1000 genomes]
rs11253424	1.00[ASN][1000 genomes]
rs11253425	1.00[ASN][1000 genomes]
rs11253430	1.00[ASN][1000 genomes]
rs11253434	1.00[ASN][1000 genomes]
rs11253435	1.00[ASN][1000 genomes]
rs11253440	1.00[ASN][1000 genomes]
rs11253441	1.00[ASN][1000 genomes]
rs11253504	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253518	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253530	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253533	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11253537	1.00[ASN][1000 genomes]
rs11253538	1.00[ASN][1000 genomes]
rs11253539	1.00[ASN][1000 genomes]
rs11253540	1.00[ASN][1000 genomes]
rs11253549	1.00[ASN][1000 genomes]
rs11253550	1.00[ASN][1000 genomes]
rs11253557	1.00[ASN][1000 genomes]
rs11253558	1.00[ASN][1000 genomes]
rs11253559	1.00[ASN][1000 genomes]
rs11253560	1.00[ASN][1000 genomes]
rs11595057	1.00[ASN][1000 genomes]
rs11595385	1.00[ASN][1000 genomes]
rs12356155	1.00[ASN][1000 genomes]
rs12356612	1.00[ASN][1000 genomes]
rs12357633	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358255	1.00[ASN][1000 genomes]
rs12359796	1.00[ASN][1000 genomes]
rs1250891	1.00[ASN][1000 genomes]
rs12761180	1.00[ASN][1000 genomes]
rs12762228	1.00[ASN][1000 genomes]
rs12762973	0.89[AFR][1000 genomes]
rs12765343	1.00[ASN][1000 genomes]
rs12768348	1.00[ASN][1000 genomes]
rs12769002	1.00[ASN][1000 genomes]
rs12770173	1.00[ASN][1000 genomes]
rs12771179	1.00[ASN][1000 genomes]
rs12771539	1.00[ASN][1000 genomes]
rs12772979	1.00[ASN][1000 genomes]
rs12773961	1.00[ASN][1000 genomes]
rs12774985	1.00[ASN][1000 genomes]
rs12777021	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12777800	1.00[ASN][1000 genomes]
rs12777801	1.00[ASN][1000 genomes]
rs12778271	1.00[ASN][1000 genomes]
rs12781100	1.00[ASN][1000 genomes]
rs12781329	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12782936	1.00[ASN][1000 genomes]
rs1536336	1.00[ASN][1000 genomes]
rs17221456	1.00[ASN][1000 genomes]
rs17221463	1.00[ASN][1000 genomes]
rs17221491	1.00[ASN][1000 genomes]
rs17293580	1.00[ASN][1000 genomes]
rs17293608	1.00[ASN][1000 genomes]
rs1871621	1.00[ASN][1000 genomes]
rs1871622	1.00[ASN][1000 genomes]
rs28512382	1.00[ASN][1000 genomes]
rs34115136	1.00[ASN][1000 genomes]
rs34159706	1.00[ASN][1000 genomes]
rs34251037	1.00[ASN][1000 genomes]
rs34270668	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34318754	1.00[ASN][1000 genomes]
rs34383514	1.00[ASN][1000 genomes]
rs34480046	1.00[ASN][1000 genomes]
rs34487581	1.00[ASN][1000 genomes]
rs34527494	1.00[ASN][1000 genomes]
rs34885925	1.00[ASN][1000 genomes]
rs34982663	1.00[ASN][1000 genomes]
rs35028518	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35306767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35363972	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35443149	1.00[ASN][1000 genomes]
rs35666723	1.00[ASN][1000 genomes]
rs35667562	1.00[ASN][1000 genomes]
rs35670857	1.00[ASN][1000 genomes]
rs35709890	1.00[ASN][1000 genomes]
rs35957139	1.00[ASN][1000 genomes]
rs35967867	1.00[ASN][1000 genomes]
rs41260144	1.00[ASN][1000 genomes]
rs55697724	1.00[ASN][1000 genomes]
rs55708963	1.00[ASN][1000 genomes]
rs55742421	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56222464	1.00[ASN][1000 genomes]
rs61830900	1.00[ASN][1000 genomes]
rs61830926	1.00[ASN][1000 genomes]
rs61830931	1.00[ASN][1000 genomes]
rs61830933	1.00[ASN][1000 genomes]
rs61831436	1.00[ASN][1000 genomes]
rs61833260	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61833265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66462130	1.00[ASN][1000 genomes]
rs66797613	1.00[ASN][1000 genomes]
rs67205460	1.00[ASN][1000 genomes]
rs67696450	1.00[ASN][1000 genomes]
rs7070876	0.87[AMR][1000 genomes]
rs7071974	1.00[ASN][1000 genomes]
rs7071982	1.00[ASN][1000 genomes]
rs7072970	1.00[ASN][1000 genomes]
rs7085476	1.00[ASN][1000 genomes]
rs7088956	1.00[ASN][1000 genomes]
rs7092353	1.00[ASN][1000 genomes]
rs7093665	1.00[ASN][1000 genomes]
rs7094031	1.00[ASN][1000 genomes]
rs72778228	1.00[ASN][1000 genomes]
rs7914758	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS 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 target site	41 gene(s)	inside rSNPs	diseases
7	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv825207	chr10:957020-1005451	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
15	nsv825208	chr10:965883-1004836	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	esv2753756	chr10:985264-1052950	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv1050577	chr10:986723-1277854	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
18	nsv540409	chr10:986723-1277854	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
19	nsv5521	chr10:986842-1031352	Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv1037193	chr10:989533-1019630	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12354914	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:989600-993400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr10:990600-991800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:990600-991800	Weak transcription	Colonic Mucosa	Colon
4	chr10:990800-993000	Weak transcription	Stomach Mucosa	stomach
5	chr10:990800-995400	Weak transcription	Lung	lung
6	chr10:991000-992200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr10:991200-991600	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links