Variant report

Variant	rs12340696
Chromosome Location	chr9:79185848-79185849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:79185829-79186977	HL-60	blood:	n/a	n/a
2	WRNIP1	chr9:79185791-79185906	GM12878	blood:	n/a	n/a
3	MAX	chr9:79185802-79186932	NB4	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:85195072..85196733-chr9:79185153..79186653,2	K562	blood:
2	chr12:34371159..34372668-chr9:79185191..79186691,2	MCF-7	breast:
3	chr21:9824031..9827240-chr9:79185229..79188221,3	K562	blood:
4	chr12:34371158..34372658-chr9:79185159..79186851,2	K562	blood:
5	chr9:79185163..79186712-chrX:108297443..108299231,2	K562	blood:
6	chr1:91851284..91852891-chr9:79185170..79186720,3	MCF-7	breast:
7	chr12:127649414..127651999-chr9:79185347..79188198,2	K562	blood:
8	chr2:133014924..133016727-chr9:79185176..79186694,2	K562	blood:
9	chr12:34371158..34372662-chr9:79185159..79186697,3	K562	blood:
10	chr21:9826010..9828651-chr9:79185182..79186853,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000241781	TF binding region
ENSG00000255652	Chromatin interaction
ENSG00000264063	Chromatin interaction
ENSG00000226958	Chromatin interaction
ENSG00000163046	Chromatin interaction
ENSG00000264462	Chromatin interaction
ENSG00000239776	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10119518	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10121652	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10123325	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10521473	1.00[EUR][1000 genomes]
rs11144991	1.00[EUR][1000 genomes]
rs11144993	1.00[EUR][1000 genomes]
rs12336287	1.00[EUR][1000 genomes]
rs12337785	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12342460	1.00[EUR][1000 genomes]
rs12344065	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12345816	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12351220	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1346041	1.00[EUR][1000 genomes]
rs17062959	1.00[EUR][1000 genomes]
rs17062964	1.00[EUR][1000 genomes]
rs17062967	1.00[EUR][1000 genomes]
rs17081141	1.00[EUR][1000 genomes]
rs17081142	1.00[EUR][1000 genomes]
rs2015354	1.00[EUR][1000 genomes]
rs28470485	1.00[EUR][1000 genomes]
rs28576740	1.00[EUR][1000 genomes]
rs28587388	1.00[EUR][1000 genomes]
rs28635278	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55725331	1.00[EUR][1000 genomes]
rs55825540	1.00[EUR][1000 genomes]
rs56026497	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56143215	1.00[EUR][1000 genomes]
rs56145880	1.00[EUR][1000 genomes]
rs56679509	1.00[EUR][1000 genomes]
rs57802610	1.00[EUR][1000 genomes]
rs60467484	1.00[EUR][1000 genomes]
rs6560530	1.00[EUR][1000 genomes]
rs7044442	1.00[EUR][1000 genomes]
rs73449878	1.00[EUR][1000 genomes]
rs73449890	1.00[EUR][1000 genomes]
rs73449896	1.00[EUR][1000 genomes]
rs73452104	1.00[EUR][1000 genomes]
rs73454158	1.00[EUR][1000 genomes]
rs73650254	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73650286	1.00[EUR][1000 genomes]
rs73650287	1.00[EUR][1000 genomes]
rs73650987	1.00[EUR][1000 genomes]
rs73650989	1.00[EUR][1000 genomes]
rs73650990	1.00[EUR][1000 genomes]
rs73650991	1.00[EUR][1000 genomes]
rs73650992	1.00[EUR][1000 genomes]
rs73650994	1.00[EUR][1000 genomes]
rs73650996	1.00[EUR][1000 genomes]
rs73650997	1.00[EUR][1000 genomes]
rs73650998	1.00[EUR][1000 genomes]
rs73650999	1.00[EUR][1000 genomes]
rs73651000	1.00[EUR][1000 genomes]
rs73651001	1.00[EUR][1000 genomes]
rs7848842	1.00[EUR][1000 genomes]
rs7850310	1.00[EUR][1000 genomes]
rs7855826	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7867080	1.00[EUR][1000 genomes]
rs7875591	1.00[EUR][1000 genomes]
rs867646	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv893480	chr9:79115844-79222584	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79176000-79186400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:79176600-79186400	Weak transcription	Brain Anterior Caudate	brain
3	chr9:79177800-79186600	Weak transcription	HSMMtube	muscle
4	chr9:79178200-79186200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:79178400-79186200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:79179600-79186200	Weak transcription	NHLF	lung
7	chr9:79179600-79186600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:79182200-79186600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:79182600-79186200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:79182600-79186200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:79182600-79186400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:79184400-79186400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:79184800-79186400	Weak transcription	Stomach Mucosa	stomach
14	chr9:79184800-79186600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:79185000-79186400	Weak transcription	Gastric	stomach
16	chr9:79185200-79186200	ZNF genes & repeats	Fetal Intestine Small	intestine
17	chr9:79185200-79186400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:79185400-79186400	Weak transcription	Brain Substantia Nigra	brain
19	chr9:79185400-79186600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
20	chr9:79185400-79187000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:79185600-79186200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr9:79185600-79186400	Weak transcription	Fetal Thymus	thymus
23	chr9:79185600-79187000	ZNF genes & repeats	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links