Variant report

Variant	rs56355079
Chromosome Location	chr6:28060398-28060399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28010916..28013781-chr6:28060247..28062544,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF165-1	chr6:28060117-28063493	NONHSAT108425
2	lnc-ZNF165-1	chr6:28060205-28060623	NONHSAT108427

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10484404	0.97[EUR][1000 genomes]
rs1150685	0.94[EUR][1000 genomes]
rs1150697	0.84[EUR][1000 genomes]
rs1890809	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2622315	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6929559	0.94[EUR][1000 genomes]
rs73396550	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73396583	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7739332	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56355079	AL022393.7	cis	Thyroid	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28049600-28063000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:28050800-28061200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:28053400-28064600	Strong transcription	Placenta	Placenta
4	chr6:28057800-28060400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:28057800-28065800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:28058000-28060400	Weak transcription	NHEK	skin
7	chr6:28058000-28060600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:28058000-28064800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:28058200-28062200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:28058200-28062200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:28058200-28072200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:28058400-28060800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:28058400-28061200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:28058800-28072000	Weak transcription	HMEC	breast
15	chr6:28059200-28061000	Weak transcription	Lung	lung
16	chr6:28059200-28061200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:28059200-28063000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:28059200-28063200	Weak transcription	Pancreas	Pancrea
19	chr6:28059200-28063400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:28059200-28066800	Weak transcription	Esophagus	oesophagus
21	chr6:28059400-28060400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr6:28059400-28061600	Weak transcription	Ovary	ovary
23	chr6:28059400-28062000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:28059400-28062000	Weak transcription	Fetal Stomach	stomach
25	chr6:28059400-28062600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:28059400-28072000	Weak transcription	Brain Substantia Nigra	brain
27	chr6:28059800-28063600	Weak transcription	Fetal Heart	heart

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