Variant report

Variant	rs1979092
Chromosome Location	chr5:118399212-118399213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:118398187..118399775-chr5:118406820..118408507,2	MCF-7	breast:
2	chr5:118396867..118401379-chr5:118402129..118406971,7	K562	blood:
3	chr5:118397443..118401188-chr5:118403593..118406456,7	K562	blood:

Variant related genes	Relation type
ENSG00000249494	Chromatin interaction
ENSG00000239011	Chromatin interaction
ENSG00000172869	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1375163	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17144918	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17144924	1.00[MEX][hapmap]
rs17144962	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs17144994	0.84[ASW][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1979093	0.88[AFR][1000 genomes]
rs2135054	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2377138	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2404394	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs28581500	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2889564	1.00[AMR][1000 genomes]
rs36086810	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36116741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6867580	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6869894	0.84[YRI][hapmap];0.87[AFR][1000 genomes]
rs6870423	0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6870607	1.00[AMR][1000 genomes]
rs6870955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6871228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6871822	0.94[AFR][1000 genomes]
rs6888039	1.00[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6889921	1.00[AMR][1000 genomes]
rs6893078	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72784072	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244805	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv882774	chr5:118325429-118553470	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1018539	chr5:118355284-118445244	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3392804	chr5:118398003-118400001	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
6	esv3371918	chr5:118398503-118399651	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118386600-118399400	Weak transcription	HSMMtube	muscle
2	chr5:118396000-118405600	Weak transcription	Primary B cells from cord blood	blood
3	chr5:118399000-118400200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr5:118399000-118400200	Enhancers	Duodenum Mucosa	Duodenum
5	chr5:118399000-118400200	Enhancers	HepG2	liver
6	chr5:118399200-118399400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:118399200-118399400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr5:118399200-118399600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:118399200-118399600	Enhancers	Primary hematopoietic stem cells	blood
10	chr5:118399200-118399600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr5:118399200-118399600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:118399200-118399600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:118399200-118399600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:118399200-118399600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr5:118399200-118399600	Enhancers	Thymus	Thymus
16	chr5:118399200-118399600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr5:118399200-118399800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:118399200-118399800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:118399200-118399800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:118399200-118399800	Enhancers	Fetal Intestine Small	intestine
21	chr5:118399200-118399800	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr5:118399200-118399800	Flanking Active TSS	GM12878-XiMat	blood
23	chr5:118399200-118399800	Enhancers	Hela-S3	cervix
24	chr5:118399200-118400000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:118399200-118400000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr5:118399200-118400000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:118399200-118400000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:118399200-118400000	Enhancers	Stomach Mucosa	stomach
29	chr5:118399200-118400200	Enhancers	Primary B cells from peripheral blood	blood
30	chr5:118399200-118400200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr5:118399200-118400200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:118399200-118400200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:118399200-118400200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr5:118399200-118400200	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr5:118399200-118400200	Enhancers	K562	blood
36	chr5:118399200-118400200	Enhancers	Osteobl	bone

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