Variant report

Variant	rs6556890
Chromosome Location	chr5:95181222-95181223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF1	chr5:95181217-95181233	K562	blood:	n/a	n/a
2	NR3C1	chr5:95181070-95181398	A549	lung:	n/a	n/a
3	NR3C1	chr5:95181066-95181367	A549	lung:	n/a	n/a
4	NR3C1	chr5:95181125-95181275	A549	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:95064544..95067364-chr5:95180646..95182818,3	MCF-7	breast:
2	chr5:95137350..95139988-chr5:95179916..95183018,3	MCF-7	breast:
3	chr5:95122048..95125672-chr5:95179642..95182375,3	MCF-7	breast:
4	chr5:95001354..95003054-chr5:95181008..95183990,2	K562	blood:
5	chr5:95175808..95177943-chr5:95180216..95182740,2	MCF-7	breast:
6	chr5:94984590..94987808-chr5:95181177..95184579,4	K562	blood:
7	chr5:94978692..94981484-chr5:95178419..95181281,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272021	TF binding region
ENSG00000164292	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10069749	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10077757	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13361485	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13361488	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2161313	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2547996	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35234911	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3756704	0.93[ASN][1000 genomes]
rs3797206	0.82[ASN][1000 genomes]
rs6873668	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6875489	0.85[ASN][1000 genomes]
rs7709560	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7725607	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs918469	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs918470	0.97[ASN][1000 genomes]
rs9314160	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95171800-95185800	Weak transcription	Pancreas	Pancrea
2	chr5:95175800-95182200	Weak transcription	Esophagus	oesophagus
3	chr5:95177000-95181400	Enhancers	Primary hematopoietic stem cells	blood
4	chr5:95177800-95192200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:95178200-95182200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:95178400-95188400	Weak transcription	Stomach Mucosa	stomach
7	chr5:95179000-95186200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:95179000-95206000	Weak transcription	Spleen	Spleen
9	chr5:95179200-95182200	Weak transcription	Thymus	Thymus
10	chr5:95179200-95182200	Weak transcription	HUVEC	blood vessel
11	chr5:95179200-95184200	Weak transcription	HSMM	muscle
12	chr5:95179200-95185800	Weak transcription	Lung	lung
13	chr5:95179400-95181400	Weak transcription	HepG2	liver
14	chr5:95179400-95181600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:95179400-95181600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:95179400-95182000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:95179400-95182200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:95179400-95182200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:95179400-95182200	Weak transcription	NHLF	lung
20	chr5:95179400-95182400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:95179400-95182400	Weak transcription	Brain Anterior Caudate	brain
22	chr5:95179400-95182400	Weak transcription	Brain Substantia Nigra	brain
23	chr5:95179400-95183000	Weak transcription	Fetal Heart	heart
24	chr5:95179400-95183600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:95179400-95184600	Weak transcription	NH-A	brain
26	chr5:95179400-95184600	Weak transcription	NHDF-Ad	bronchial
27	chr5:95179600-95182000	Weak transcription	Osteobl	bone
28	chr5:95179600-95183000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr5:95179600-95184400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:95179800-95185200	Weak transcription	Left Ventricle	heart
31	chr5:95180000-95182200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:95180000-95182400	Weak transcription	Fetal Intestine Small	intestine
33	chr5:95180000-95182400	Weak transcription	A549	lung
34	chr5:95180000-95182600	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:95180000-95186000	Weak transcription	Right Atrium	heart
36	chr5:95180200-95182000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:95180200-95184600	Weak transcription	Adipose Nuclei	Adipose
38	chr5:95180400-95181400	Active TSS	Liver	Liver
39	chr5:95180400-95182400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:95180800-95182000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr5:95180800-95182200	Weak transcription	Psoas Muscle	Psoas
42	chr5:95180800-95182400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr5:95181000-95181400	Enhancers	K562	blood
44	chr5:95181000-95182000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:95181200-95181400	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr5:95181200-95182400	Weak transcription	Placenta	Placenta
47	chr5:95181200-95182800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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