Variant report

Variant	rs12359796
Chromosome Location	chr10:1021479-1021480
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:1020473..1022394-chr10:1030542..1032536,2	K562	blood:
2	chr10:1018775..1022710-chr10:1032776..1036101,4	K562	blood:
3	chr10:1019967..1021680-chr10:1093563..1096115,2	MCF-7	breast:
4	chr10:1000614..1004584-chr10:1019814..1022470,3	K562	blood:
5	chr10:1019761..1022243-chr10:1028840..1032476,4	MCF-7	breast:
6	chr10:976040..979233-chr10:1016379..1022615,6	MCF-7	breast:
7	chr10:1019010..1021511-chr10:1021947..1027823,6	MCF-7	breast:
8	chr10:1019821..1022788-chr10:1029841..1033519,4	MCF-7	breast:
9	chr10:975132..982582-chr10:1010670..1022073,17	MCF-7	breast:
10	chr10:1000614..1004584-chr10:1019814..1022762,4	K562	blood:
11	chr10:1019866..1021574-chr10:1021848..1023502,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000107937	Chromatin interaction
ENSG00000067064	Chromatin interaction
ENSG00000229869	Chromatin interaction
ENSG00000047056	Chromatin interaction
ENSG00000107929	Chromatin interaction
ENSG00000205740	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1013504	1.00[ASN][1000 genomes]
rs10508206	0.83[CEU][hapmap]
rs10903358	1.00[ASN][1000 genomes]
rs11250228	1.00[CEU][hapmap]
rs11253504	1.00[ASN][1000 genomes]
rs11253518	1.00[ASN][1000 genomes]
rs11253530	1.00[ASN][1000 genomes]
rs11253537	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253538	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253539	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253540	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253550	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253557	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253558	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253559	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253560	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354914	1.00[ASN][1000 genomes]
rs12356612	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357633	1.00[ASN][1000 genomes]
rs1250891	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761180	1.00[ASN][1000 genomes]
rs12762228	1.00[ASN][1000 genomes]
rs12762955	0.83[CEU][hapmap]
rs12768348	1.00[ASN][1000 genomes]
rs12769002	1.00[ASN][1000 genomes]
rs12770173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12770910	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12771179	1.00[ASN][1000 genomes]
rs12771539	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772979	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773961	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774985	1.00[ASN][1000 genomes]
rs12777021	1.00[ASN][1000 genomes]
rs12777788	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12777800	1.00[ASN][1000 genomes]
rs12777801	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12778271	1.00[ASN][1000 genomes]
rs12781100	1.00[ASN][1000 genomes]
rs12781329	1.00[ASN][1000 genomes]
rs17221456	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17221463	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17221491	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs17293580	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17293608	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871621	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871622	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28512382	1.00[ASN][1000 genomes]
rs34115136	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34159706	1.00[ASN][1000 genomes]
rs34251037	1.00[ASN][1000 genomes]
rs34270668	1.00[ASN][1000 genomes]
rs34318754	1.00[ASN][1000 genomes]
rs34480046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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	1.00[ASN][1000 genomes]
rs35306767	1.00[ASN][1000 genomes]
rs35363972	1.00[ASN][1000 genomes]
rs35443149	1.00[ASN][1000 genomes]
rs35666723	1.00[ASN][1000 genomes]
rs35667562	1.00[ASN][1000 genomes]
rs35670857	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];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	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	1.00[ASN][1000 genomes]
rs61833265	1.00[ASN][1000 genomes]
rs66462130	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66797613	1.00[ASN][1000 genomes]
rs67205460	1.00[ASN][1000 genomes]
rs67696450	1.00[ASN][1000 genomes]
rs7088956	1.00[ASN][1000 genomes]
rs7093665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094031	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72778228	1.00[ASN][1000 genomes]
rs7914758	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	nsv949405	chr10:1010464-1376105	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
18	nsv525014	chr10:1013535-1024214	Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
19	nsv1048254	chr10:1016006-1146595	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
20	esv1812809	chr10:1021156-1051728	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
21	esv1813158	chr10:1021156-1062915	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
22	esv1831483	chr10:1021156-1062915	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12359796	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:998800-1026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:1014800-1022400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:1016000-1021600	Enhancers	Stomach Mucosa	stomach
4	chr10:1017000-1022400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr10:1017000-1022600	Weak transcription	Ovary	ovary
6	chr10:1017600-1023800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr10:1017800-1022600	Weak transcription	HSMM	muscle
8	chr10:1017800-1022600	Weak transcription	NHLF	lung
9	chr10:1017800-1023600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr10:1017800-1024600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr10:1017800-1024800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr10:1018000-1022400	Weak transcription	Fetal Muscle Leg	muscle
13	chr10:1018000-1022400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr10:1018000-1023800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr10:1018000-1024400	Weak transcription	Adipose Nuclei	Adipose
16	chr10:1018400-1025000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr10:1019200-1022000	Weak transcription	Lung	lung
18	chr10:1019200-1022200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:1019400-1030800	Weak transcription	Gastric	stomach
20	chr10:1020000-1021800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:1020200-1025000	Weak transcription	Osteobl	bone
22	chr10:1020600-1024600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr10:1020800-1022600	Weak transcription	Fetal Intestine Large	intestine
24	chr10:1021000-1022000	Weak transcription	Fetal Intestine Small	intestine
25	chr10:1021000-1022400	Weak transcription	Pancreas	Pancrea
26	chr10:1021000-1022800	Weak transcription	Fetal Lung	lung
27	chr10:1021400-1023600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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