Variant report

Variant	rs73918423
Chromosome Location	chr2:12172190-12172191
allele	A/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	POLR2A	chr2:12171335-12176486	GM12891	blood:	n/a	n/a
2	TCF3	chr2:12172043-12172335	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:12171416-12174858	Raji	blood:	n/a	n/a
4	EP300	chr2:12172017-12172276	GM12878	blood:	n/a	n/a
5	EBF1	chr2:12172152-12172932	GM12878	blood:	n/a	n/a
6	MAX	chr2:12172133-12172380	GM12878	blood:	n/a	chr2:12172301-12172310 chr2:12172302-12172309
7	MXI1	chr2:12172152-12172307	GM12878	blood:	n/a	n/a
8	POU2F2	chr2:12171908-12172406	GM12878	blood:	n/a	n/a
9	PAX5	chr2:12172021-12172378	GM12878	blood:	n/a	chr2:12172184-12172201
10	EBF1	chr2:12171968-12172379	GM12878	blood:	n/a	n/a
11	EBF1	chr2:12172076-12172337	GM12878	blood:	n/a	n/a
12	EP300	chr2:12171972-12172992	GM12878	blood:	n/a	chr2:12172780-12172794
13	GATA1	chr2:12171642-12172956	PBDE	blood:	n/a	n/a
14	POU2F2	chr2:12172043-12172376	GM12891	blood:	n/a	n/a
15	BHLHE40	chr2:12171965-12172981	GM12878	blood:	n/a	n/a
16	PAX5	chr2:12172032-12172325	GM12878	blood:	n/a	chr2:12172184-12172201
17	RUNX3	chr2:12171887-12172336	GM12878	blood:	n/a	n/a
18	RUNX3	chr2:12171871-12172389	GM12878	blood:	n/a	n/a
19	CHD2	chr2:12172106-12172982	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:12172190-12172320	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000238503	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12463701	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12464227	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12469736	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12471363	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12475585	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12476249	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28420399	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56260961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59609793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60195725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60873627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73915889	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73915899	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73915902	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73918407	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73918410	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73918411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73918413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73918415	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73918416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73918422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73918424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73918425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73918426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73918427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73918432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73918434	0.90[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	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv999704	chr2:12153766-12243960	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1005069	chr2:12161023-12242734	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1000696	chr2:12162843-12241022	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12167600-12172400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:12171200-12172400	Enhancers	Primary B cells from cord blood	blood
3	chr2:12171200-12178000	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:12171400-12173600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:12171600-12172400	Enhancers	Gastric	stomach
6	chr2:12171600-12172800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:12171600-12173400	Flanking Active TSS	GM12878-XiMat	blood
8	chr2:12171800-12172400	Enhancers	Fetal Heart	heart
9	chr2:12171800-12172400	Enhancers	Stomach Mucosa	stomach
10	chr2:12171800-12172400	Enhancers	K562	blood
11	chr2:12172000-12172400	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:12172000-12172400	Bivalent Enhancer	Fetal Brain Male	brain
13	chr2:12172000-12172400	Enhancers	Left Ventricle	heart
14	chr2:12172000-12173400	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links