Variant report

Variant	rs11111960
Chromosome Location	chr12:104657126-104657127
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	GATA3	chr12:104657046-104658213	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr12:104656930-104658314	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr12:104657122-104658098	SK-N-SH	brain:	n/a	chr12:104657311-104657320
4	GATA3	chr12:104657048-104658232	SK-N-SH	brain:	n/a	n/a
5	PBX3	chr12:104657016-104658202	SK-N-SH	brain:	n/a	chr12:104657311-104657320
6	TCF12	chr12:104656931-104658292	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr12:104657100-104657609	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104654376..104656180-chr12:104656602..104658713,2	K562	blood:

Variant related genes	Relation type
RPL18AP3	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10735392	0.83[JPT][hapmap]
rs10735393	0.91[JPT][hapmap]
rs10745995	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10745996	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10745997	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10745998	0.81[ASN][1000 genomes]
rs10778311	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10778315	0.89[ASN][1000 genomes]
rs10778316	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10778317	0.82[ASN][1000 genomes]
rs10778318	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10778323	0.83[JPT][hapmap]
rs10861169	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs10861180	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs10861187	0.89[GIH][hapmap]
rs10861197	0.87[GIH][hapmap]
rs10861202	0.84[EUR][1000 genomes]
rs10861204	0.83[JPT][hapmap]
rs11111959	0.95[ASN][1000 genomes]
rs11111962	0.90[ASN][1000 genomes]
rs11111963	0.81[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11111987	0.91[GIH][hapmap]
rs12424869	1.00[JPT][hapmap]
rs17035324	0.81[JPT][hapmap]
rs28626346	0.85[ASN][1000 genomes]
rs4129598	0.81[JPT][hapmap]
rs4246264	0.81[JPT][hapmap]
rs4246267	0.82[ASN][1000 genomes]
rs4246269	0.83[JPT][hapmap]
rs4246271	0.83[JPT][hapmap]
rs4254139	0.82[ASN][1000 genomes]
rs4329742	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4406890	0.81[JPT][hapmap]
rs4475991	0.91[CHB][hapmap]
rs4545635	0.81[JPT][hapmap]
rs4569072	0.88[ASN][1000 genomes]
rs4964260	0.81[JPT][hapmap]
rs4964288	0.83[JPT][hapmap]
rs4964735	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4964752	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4964761	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4964779	0.83[JPT][hapmap]
rs4964782	0.87[GIH][hapmap]
rs5018287	0.87[GIH][hapmap]
rs6539138	0.83[JPT][hapmap]
rs7137305	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138523	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7294778	0.91[GIH][hapmap]
rs7294997	0.90[JPT][hapmap]
rs7295751	0.82[ASN][1000 genomes]
rs7301631	0.91[JPT][hapmap]
rs7313063	0.91[CHB][hapmap]
rs7342395	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs7488680	0.91[GIH][hapmap]
rs7975161	0.81[JPT][hapmap]
rs9668964	0.90[ASN][1000 genomes]
rs9739833	0.83[JPT][hapmap]

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	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats 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
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 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	chr12:104649800-104657200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:104652000-104669600	Weak transcription	Hela-S3	cervix
3	chr12:104652800-104673000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr12:104656000-104657200	Enhancers	NHEK	skin
5	chr12:104656200-104657400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:104656200-104658200	Enhancers	A549	lung
7	chr12:104656200-104658400	Enhancers	HMEC	breast
8	chr12:104656400-104658200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:104656400-104658200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:104656600-104658200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:104656800-104657600	Enhancers	Fetal Thymus	thymus
12	chr12:104656800-104658000	Enhancers	Stomach Mucosa	stomach
13	chr12:104656800-104658200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:104656800-104658200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:104656800-104658200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:104656800-104658200	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr12:104656800-104658600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:104657000-104658200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr12:104657000-104658200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:104657000-104658200	Enhancers	HSMM	muscle
21	chr12:104657000-104658200	Enhancers	NHLF	lung
22	chr12:104657000-104658400	Enhancers	HSMMtube	muscle
23	chr12:104657000-104658800	Enhancers	NHDF-Ad	bronchial

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