Variant report

Variant	rs10778318
Chromosome Location	chr12:104671506-104671507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104669706..104671743-chr12:104681393..104683576,2	K562	blood:
2	chr12:104657761..104659817-chr12:104670354..104673029,2	MCF-7	breast:
3	chr12:104668998..104671524-chr12:104672652..104674551,2	K562	blood:
4	chr12:104671228..104673163-chr12:104680722..104683661,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction
ENSG00000257732	Chromatin interaction
ENSG00000213442	Chromatin interaction

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	1.00[JPT][hapmap]
rs10745996	1.00[JPT][hapmap]
rs10745997	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10745998	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10778311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10778315	0.86[ASN][1000 genomes]
rs10778316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778317	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778323	0.83[JPT][hapmap]
rs10861169	0.81[JPT][hapmap]
rs10861204	0.83[JPT][hapmap]
rs11111960	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11111962	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111970	0.87[AFR][1000 genomes]
rs11111973	0.95[AFR][1000 genomes]
rs12303195	0.80[AMR][1000 genomes]
rs12368657	0.90[AFR][1000 genomes]
rs12424869	1.00[JPT][hapmap]
rs17035324	0.81[JPT][hapmap]
rs28534514	0.91[AFR][1000 genomes]
rs28626346	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129598	0.81[JPT][hapmap]
rs4246264	0.81[JPT][hapmap]
rs4246267	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246269	0.83[JPT][hapmap]
rs4246271	0.83[JPT][hapmap]
rs4254139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329742	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4406890	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs4545635	0.81[JPT][hapmap]
rs4569072	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4964260	0.81[JPT][hapmap]
rs4964288	0.83[JPT][hapmap]
rs4964728	0.89[CHB][hapmap]
rs4964735	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4964752	1.00[JPT][hapmap]
rs4964753	0.88[AFR][1000 genomes]
rs4964761	1.00[JPT][hapmap]
rs4964779	0.83[JPT][hapmap]
rs6539138	0.83[JPT][hapmap]
rs7136838	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137305	0.82[ASN][1000 genomes]
rs7138523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294997	0.90[JPT][hapmap]
rs7295751	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301631	0.91[JPT][hapmap]
rs7342321	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7342395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957725	0.89[CHB][hapmap]
rs7969435	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975161	0.81[JPT][hapmap]
rs9668964	0.87[ASN][1000 genomes]
rs9738677	0.84[AMR][1000 genomes];0.81[EUR][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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104652800-104673000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr12:104658200-104672800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:104664600-104673200	Weak transcription	HSMM	muscle
4	chr12:104667600-104679600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:104669600-104671800	Enhancers	NH-A	brain
6	chr12:104669800-104672800	Enhancers	HUVEC	blood vessel
7	chr12:104670000-104674000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:104670200-104671800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr12:104670400-104671600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:104670400-104672800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:104670400-104674000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr12:104670400-104674200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:104670400-104679600	Weak transcription	Thymus	Thymus
14	chr12:104670600-104671800	Enhancers	HepG2	liver
15	chr12:104670600-104671800	Enhancers	NHEK	skin
16	chr12:104670600-104671800	Enhancers	Osteobl	bone
17	chr12:104670600-104672800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:104670600-104672800	Weak transcription	HSMMtube	muscle
19	chr12:104670600-104672800	Weak transcription	NHLF	lung
20	chr12:104670600-104673200	Weak transcription	HMEC	breast
21	chr12:104670600-104673200	Weak transcription	K562	blood
22	chr12:104670600-104674000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:104670600-104674000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:104670600-104679600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:104670600-104679800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:104670800-104671800	Active TSS	A549	lung
27	chr12:104671000-104671600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:104671000-104671800	Enhancers	NHDF-Ad	bronchial
29	chr12:104671200-104671600	Enhancers	Fetal Intestine Small	intestine
30	chr12:104671400-104671600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:104671400-104671600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:104671400-104671600	Enhancers	Stomach Mucosa	stomach
33	chr12:104671400-104671600	Active TSS	Hela-S3	cervix
34	chr12:104671400-104671800	Active TSS	Duodenum Mucosa	Duodenum
35	chr12:104671400-104672800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:104671400-104673400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:104671400-104674200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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