Variant report

Variant	rs4788561
Chromosome Location	chr16:71878255-71878256
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71841032..71844957-chr16:71878188..71881982,18	MCF-7	breast:
2	chr16:71840441..71845295-chr16:71875076..71881716,14	K562	blood:
3	chr16:71878006..71880307-chr16:74330687..74332965,2	MCF-7	breast:
4	chr16:71841284..71844520-chr16:71878157..71881366,4	K562	blood:
5	chr16:71874199..71877038-chr16:71877989..71879854,2	MCF-7	breast:
6	chr16:71877290..71879173-chr16:71916547..71919172,2	MCF-7	breast:
7	chr16:71832833..71836832-chr16:71876405..71879704,4	K562	blood:

Variant related genes	Relation type
ENSG00000166747	Chromatin interaction
ENSG00000103035	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11075910	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12444594	0.91[EUR][1000 genomes]
rs12447045	0.80[AFR][1000 genomes]
rs17286411	0.89[AFR][1000 genomes]
rs1834036	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2288030	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35619990	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4788450	0.85[EUR][1000 genomes]
rs4788568	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4788569	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4788575	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4788579	0.87[EUR][1000 genomes]
rs8044004	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8044335	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9932707	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71870800-71879000	Weak transcription	NHEK	skin
2	chr16:71871400-71879000	Weak transcription	HMEC	breast
3	chr16:71871600-71879200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr16:71874600-71879000	Weak transcription	Hela-S3	cervix
5	chr16:71874800-71878800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr16:71875400-71879000	Enhancers	Primary B cells from peripheral blood	blood
7	chr16:71876000-71879400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr16:71876200-71878400	Flanking Active TSS	GM12878-XiMat	blood
9	chr16:71876200-71878800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr16:71876200-71879000	Weak transcription	Fetal Thymus	thymus
11	chr16:71876400-71879000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr16:71876400-71879200	Weak transcription	Esophagus	oesophagus
13	chr16:71876400-71879200	Weak transcription	Placenta	Placenta
14	chr16:71876600-71879000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr16:71876600-71879000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr16:71876600-71879000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr16:71876600-71879000	Weak transcription	K562	blood
18	chr16:71876600-71879200	Weak transcription	Primary T cells from cord blood	blood
19	chr16:71876800-71878800	Weak transcription	HepG2	liver
20	chr16:71876800-71879000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr16:71876800-71879000	Weak transcription	Primary B cells from cord blood	blood
22	chr16:71877000-71879000	Weak transcription	Pancreas	Pancrea
23	chr16:71877000-71879400	Weak transcription	Fetal Heart	heart
24	chr16:71877800-71879000	Weak transcription	Fetal Kidney	kidney
25	chr16:71878000-71878400	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links