Variant report

Variant	rs28473019
Chromosome Location	chr16:48402383-48402384
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr16:48402306-48402701	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:48390430..48396082-chr16:48398412..48402671,6	MCF-7	breast:
2	chr16:48402282..48407133-chr16:48417266..48420023,6	MCF-7	breast:
3	chr16:48399757..48401408-chr16:48401454..48403531,2	K562	blood:
4	chr16:48396253..48404408-chr16:48411826..48421166,27	K562	blood:

Variant related genes	Relation type
SIAH1	TF binding region
ENSG00000196470	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs13332870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13335175	1.00[AMR][1000 genomes]
rs13336203	1.00[AMR][1000 genomes]
rs13336441	1.00[AMR][1000 genomes]
rs13336832	1.00[AMR][1000 genomes]
rs13337923	1.00[AMR][1000 genomes]
rs28361908	1.00[AMR][1000 genomes]
rs28379458	1.00[AMR][1000 genomes]
rs28539217	1.00[AMR][1000 genomes]
rs28599555	1.00[AMR][1000 genomes]
rs28661941	1.00[AMR][1000 genomes]
rs28848294	1.00[AMR][1000 genomes]
rs9924578	0.90[AFR][1000 genomes]
rs9926437	1.00[AMR][1000 genomes]
rs9926749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9927124	1.00[AMR][1000 genomes]
rs9928527	1.00[AMR][1000 genomes]
rs9929780	1.00[AMR][1000 genomes]
rs9930404	0.90[AFR][1000 genomes]
rs9931267	1.00[AMR][1000 genomes]
rs9931866	1.00[AMR][1000 genomes]
rs9932677	1.00[AMR][1000 genomes]
rs9933958	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9934175	1.00[AMR][1000 genomes]
rs9934459	1.00[AMR][1000 genomes]
rs9934918	1.00[AMR][1000 genomes]
rs9936494	1.00[AMR][1000 genomes]
rs9936636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9936892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9938115	1.00[AMR][1000 genomes]
rs9938350	1.00[AMR][1000 genomes]
rs9938594	1.00[AMR][1000 genomes]
rs9940237	1.00[AMR][1000 genomes]
rs9941354	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv1821072	chr16:48268318-48504364	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv833219	chr16:48290595-48459301	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1061708	chr16:48304343-48482594	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv542917	chr16:48304343-48482594	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv2758424	chr16:48329437-48479754	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv2758645	chr16:48329437-48479754	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	esv1837150	chr16:48375777-48470715	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	esv1802902	chr16:48394626-48419662	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
10	esv1836876	chr16:48395527-48459558	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	esv1842331	chr16:48395527-48459558	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48400200-48404200	Weak transcription	Spleen	Spleen
2	chr16:48400200-48409000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:48400400-48404800	Weak transcription	Pancreas	Pancrea
4	chr16:48400600-48403600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr16:48400600-48417600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr16:48400800-48402400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr16:48400800-48402400	Enhancers	Brain Substantia Nigra	brain
8	chr16:48400800-48403800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr16:48400800-48404000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr16:48400800-48404200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr16:48400800-48406600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr16:48400800-48417800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:48401000-48402400	Enhancers	Hela-S3	cervix
14	chr16:48401000-48402600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr16:48401000-48403600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr16:48401000-48404400	Weak transcription	Esophagus	oesophagus
17	chr16:48401000-48404600	Weak transcription	Lung	lung
18	chr16:48401000-48404600	Weak transcription	Ovary	ovary
19	chr16:48401000-48405000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr16:48401000-48406800	Weak transcription	Right Atrium	heart
21	chr16:48401000-48407400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr16:48401000-48412600	Weak transcription	Thymus	Thymus
23	chr16:48401200-48403400	Weak transcription	Placenta	Placenta
24	chr16:48401200-48404000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr16:48401200-48404600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr16:48401200-48404600	Weak transcription	Left Ventricle	heart
27	chr16:48401200-48409000	Weak transcription	Gastric	stomach
28	chr16:48401400-48403400	Weak transcription	Psoas Muscle	Psoas
29	chr16:48401400-48404000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr16:48401400-48406800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr16:48401400-48406800	Weak transcription	Fetal Muscle Leg	muscle
32	chr16:48401400-48407000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr16:48401400-48407000	Weak transcription	Fetal Kidney	kidney
34	chr16:48401400-48407400	Weak transcription	Aorta	Aorta
35	chr16:48401400-48408400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr16:48401400-48408400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr16:48401600-48403200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr16:48401600-48404000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr16:48401600-48404200	Weak transcription	Right Ventricle	heart
40	chr16:48401600-48406200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr16:48401600-48406400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr16:48401600-48406600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr16:48401600-48407400	Weak transcription	HSMM	muscle
44	chr16:48401600-48407600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr16:48401600-48407800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr16:48401600-48412400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr16:48401800-48403400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr16:48401800-48403400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr16:48401800-48404000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr16:48401800-48404800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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