Variant report

Variant	rs12133599
Chromosome Location	chr1:224366533-224366534
allele	C/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	GATA3	chr1:224366370-224367046	MCF-7	breast:	n/a	chr1:224366594-224366615 chr1:224366597-224366613

No.	Distal block	Cell Line	Cell type
1	chr1:224365921..224368193-chr1:224369712..224372520,2	MCF-7	breast:
2	chr1:224365629..224367265-chr1:224369608..224372554,2	K562	blood:
3	chr1:224364638..224368268-chr1:224368914..224372684,7	K562	blood:
4	chr1:224301824..224303982-chr1:224364171..224366941,2	K562	blood:

Variant related genes	Relation type
ENSG00000201898	TF binding region
DEGS1	TF binding region
ENSG00000236773	TF binding region
ENSG00000143753	Chromatin interaction
ENSG00000143756	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10799491	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10799507	1.00[EUR][1000 genomes]
rs10799543	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10916458	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10916462	0.96[EUR][1000 genomes]
rs10916472	0.92[EUR][1000 genomes]
rs10916481	0.82[EUR][1000 genomes]
rs10916497	0.88[EUR][1000 genomes]
rs10916498	0.85[EUR][1000 genomes]
rs12082619	0.88[EUR][1000 genomes]
rs12083770	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12117480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12120308	0.92[EUR][1000 genomes]
rs12124547	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12126765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12126815	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12128376	1.00[AFR][1000 genomes]
rs12138866	0.96[EUR][1000 genomes]
rs12140137	0.96[EUR][1000 genomes]
rs12184283	0.88[EUR][1000 genomes]
rs45583539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56105022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60256604	0.92[EUR][1000 genomes]
rs6660194	0.92[EUR][1000 genomes]
rs6686449	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6694451	1.00[CEU][hapmap]
rs6701036	0.85[EUR][1000 genomes]
rs68073536	0.85[EUR][1000 genomes]
rs72751651	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72753956	1.00[EUR][1000 genomes]
rs72753969	1.00[EUR][1000 genomes]
rs72753980	0.91[EUR][1000 genomes]
rs72753994	0.92[EUR][1000 genomes]
rs72754000	0.96[EUR][1000 genomes]
rs72754001	0.88[EUR][1000 genomes]
rs72755905	0.96[EUR][1000 genomes]
rs7514140	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7552239	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv8857	chr1:224359943-224383023	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12133599	CNIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224346400-224370000	Weak transcription	Esophagus	oesophagus
2	chr1:224359000-224369200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:224359000-224369200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:224359000-224370200	Weak transcription	Small Intestine	intestine
5	chr1:224362800-224369600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:224363400-224369600	Weak transcription	Fetal Intestine Large	intestine
7	chr1:224363400-224370000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:224363600-224370000	Weak transcription	HMEC	breast
9	chr1:224363800-224367200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:224363800-224368000	Weak transcription	Fetal Thymus	thymus
11	chr1:224363800-224368400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:224363800-224368600	Weak transcription	NHEK	skin
13	chr1:224363800-224368800	Weak transcription	Primary B cells from cord blood	blood
14	chr1:224363800-224369000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:224363800-224369600	Weak transcription	Thymus	Thymus
16	chr1:224363800-224369800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:224363800-224369800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:224363800-224369800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:224363800-224369800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:224363800-224369800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr1:224363800-224370000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:224363800-224370000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:224363800-224370000	Weak transcription	Brain Anterior Caudate	brain
24	chr1:224363800-224370200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:224363800-224370200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:224363800-224370200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:224363800-224370200	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:224363800-224370200	Weak transcription	Brain Substantia Nigra	brain
29	chr1:224363800-224370400	Weak transcription	Lung	lung
30	chr1:224364000-224367000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:224364000-224368800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:224364600-224369200	Weak transcription	Placenta	Placenta
33	chr1:224365800-224368600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:224365800-224368600	Weak transcription	HepG2	liver
35	chr1:224366400-224370000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:224366400-224370000	Weak transcription	Osteobl	bone

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