Variant report

Variant	rs13101486
Chromosome Location	chr4:21306185-21306186
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	JUND	chr4:21306181-21306485	HepG2	liver:	n/a	chr4:21306327-21306338 chr4:21306329-21306341 chr4:21306329-21306340 chr4:21306330-21306340 chr4:21306331-21306340
2	MAX	chr4:21305946-21306310	H1-hESC	embryonic stem cell:	n/a	chr4:21306083-21306092
3	JUND	chr4:21306077-21306336	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr4:21305614-21306307	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3A	chr4:21305687-21306283	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PACRGL-2	chr4:21306165-21306236	ENSG00000250243.2

Variant related genes	Relation type
KCNIP4	TF binding region

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11734360	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs12643751	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs13108412	1.00[CHB][hapmap]
rs13108702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13111015	0.91[ASN][1000 genomes]
rs13118906	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap]
rs13120431	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16870771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2007762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4696975	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap]
rs983071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1013365	chr4:20834054-21609078	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1014062	chr4:21270358-21479027	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv437914	chr4:21292213-21375817	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1005453	chr4:21295066-21454143	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21305000-21306400	Active TSS	Brain Anterior Caudate	brain
2	chr4:21305200-21306400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:21305400-21306200	Active TSS	Brain Substantia Nigra	brain
4	chr4:21305400-21306400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:21305400-21306400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:21305400-21306400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:21305400-21306400	Active TSS	Brain Angular Gyrus	brain
8	chr4:21305400-21306400	Active TSS	Brain Cingulate Gyrus	brain
9	chr4:21305400-21306400	Active TSS	Brain Germinal Matrix	brain
10	chr4:21305400-21306400	Active TSS	Fetal Brain Female	brain
11	chr4:21305600-21306200	Active TSS	H1 Cell Line	embryonic stem cell
12	chr4:21305600-21306200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:21305600-21306200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr4:21305600-21306200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr4:21305600-21306200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr4:21305600-21306200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:21305600-21306200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:21305600-21306200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
19	chr4:21305600-21306200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:21305600-21306200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:21305600-21306200	Active TSS	Brain Hippocampus Middle	brain
22	chr4:21305600-21306400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr4:21305600-21306400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:21305600-21306400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr4:21305600-21306400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr4:21305600-21306400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:21305600-21306400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr4:21305600-21306400	Bivalent/Poised TSS	Fetal Lung	lung
29	chr4:21305600-21306400	Active TSS	Ovary	ovary
30	chr4:21305800-21306200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr4:21305800-21306200	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:21305800-21306200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:21305800-21306200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:21305800-21306200	Bivalent/Poised TSS	Fetal Stomach	stomach
35	chr4:21305800-21306200	Flanking Active TSS	Gastric	stomach
36	chr4:21305800-21306200	Enhancers	Spleen	Spleen
37	chr4:21305800-21306400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:21305800-21306400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:21305800-21306400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
40	chr4:21305800-21306400	Bivalent/Poised TSS	Fetal Kidney	kidney
41	chr4:21306000-21306200	Bivalent/Poised TSS	Esophagus	oesophagus
42	chr4:21306000-21306200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr4:21306000-21306200	Bivalent Enhancer	Stomach Mucosa	stomach
44	chr4:21306000-21306400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:21306000-21306400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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