Variant report

Variant	rs10778316
Chromosome Location	chr12:104669931-104669932
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	chr12:104668426..104670566-chr12:104680778..104683191,4	MCF-7	breast:
3	chr12:104668134..104671112-chr12:104674176..104678107,3	MCF-7	breast:
4	chr12:104668998..104671524-chr12:104672652..104674551,2	K562	blood:

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction
ENSG00000257732	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10735393	0.89[JPT][hapmap]
rs10745995	1.00[JPT][hapmap]
rs10745996	1.00[JPT][hapmap]
rs10745997	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10745998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10778311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10778315	0.86[ASN][1000 genomes]
rs10778317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778318	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]
rs10861169	0.88[JPT][hapmap]
rs11111960	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11111962	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11111970	0.91[AFR][1000 genomes]
rs11111973	0.90[AFR][1000 genomes]
rs12303195	0.80[AMR][1000 genomes]
rs12368657	0.94[AFR][1000 genomes]
rs12424869	1.00[JPT][hapmap]
rs17035324	0.88[JPT][hapmap]
rs28534514	0.94[AFR][1000 genomes]
rs28626346	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34494070	0.81[AFR][1000 genomes]
rs4129598	0.88[JPT][hapmap]
rs4246264	0.88[JPT][hapmap]
rs4246267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4254139	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329742	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4388968	0.85[JPT][hapmap]
rs4406890	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs4545635	0.88[JPT][hapmap]
rs4569072	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4964260	0.88[JPT][hapmap]
rs4964728	0.85[CHB][hapmap]
rs4964735	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4964752	1.00[JPT][hapmap]
rs4964753	0.91[AFR][1000 genomes]
rs4964761	1.00[JPT][hapmap]
rs7136838	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137305	0.82[ASN][1000 genomes]
rs7138523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7294997	0.86[JPT][hapmap]
rs7295751	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301631	0.89[JPT][hapmap]
rs7342321	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7342395	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957725	0.85[CHB][hapmap]
rs7969435	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975161	0.88[JPT][hapmap]
rs9668964	0.87[ASN][1000 genomes]
rs9738677	0.84[AMR][1000 genomes];0.82[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	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:44 , 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	chr12:104658200-104670000	Weak transcription	NHLF	lung
3	chr12:104658200-104670200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:104658200-104670200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:104658200-104672800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:104663600-104670000	Weak transcription	Brain Substantia Nigra	brain
7	chr12:104664600-104673200	Weak transcription	HSMM	muscle
8	chr12:104667200-104670000	Weak transcription	K562	blood
9	chr12:104667600-104679600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:104668600-104670000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:104668600-104670000	Enhancers	HMEC	breast
12	chr12:104668600-104670600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:104669400-104670000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:104669400-104670000	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:104669400-104670800	Flanking Active TSS	A549	lung
16	chr12:104669600-104670000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:104669600-104670000	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr12:104669600-104670600	Flanking Active TSS	GM12878-XiMat	blood
19	chr12:104669600-104671800	Enhancers	NH-A	brain
20	chr12:104669800-104670000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:104669800-104670000	Enhancers	Primary B cells from cord blood	blood
22	chr12:104669800-104670000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:104669800-104670000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:104669800-104670000	Enhancers	Colonic Mucosa	Colon
25	chr12:104669800-104670000	Active TSS	Duodenum Mucosa	Duodenum
26	chr12:104669800-104670000	Enhancers	Rectal Smooth Muscle	rectum
27	chr12:104669800-104670000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr12:104669800-104670000	Flanking Active TSS	Stomach Mucosa	stomach
29	chr12:104669800-104670000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr12:104669800-104670000	Enhancers	Osteobl	bone
31	chr12:104669800-104670200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:104669800-104670400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr12:104669800-104670400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr12:104669800-104670600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr12:104669800-104670600	Enhancers	Fetal Heart	heart
36	chr12:104669800-104670600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr12:104669800-104670600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr12:104669800-104670600	Active TSS	Stomach Smooth Muscle	stomach
39	chr12:104669800-104670600	Flanking Active TSS	HepG2	liver
40	chr12:104669800-104670600	Enhancers	NHDF-Ad	bronchial
41	chr12:104669800-104670600	Flanking Active TSS	NHEK	skin
42	chr12:104669800-104670800	Flanking Active TSS	Hela-S3	cervix
43	chr12:104669800-104671000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr12:104669800-104672800	Enhancers	HUVEC	blood vessel

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