Variant report

Variant	rs28583078
Chromosome Location	chr4:659371-659372
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	chr4:659237-659464	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:658187..662144-chr4:672176..676426,5	MCF-7	breast:
2	chr4:604595..606902-chr4:659011..661677,2	MCF-7	breast:
3	chr4:540175..542143-chr4:659045..660940,2	K562	blood:
4	chr4:644054..646414-chr4:656838..659721,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272927	TF binding region
ENSG00000215375	Chromatin interaction
ENSG00000133256	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10027549	1.00[ASN][1000 genomes]
rs10027866	0.85[MKK][hapmap]
rs10030136	1.00[ASN][1000 genomes]
rs1135375	1.00[ASN][1000 genomes]
rs13119162	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28374488	0.82[ASW][hapmap];0.84[MKK][hapmap]
rs28470912	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs28483373	1.00[ASN][1000 genomes]
rs28488910	1.00[ASN][1000 genomes]
rs28525003	1.00[ASN][1000 genomes]
rs28568555	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569875	1.00[ASN][1000 genomes]
rs28573204	1.00[ASN][1000 genomes]
rs28586910	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28630797	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28742266	1.00[ASN][1000 genomes]
rs28742899	1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864130	1.00[CHD][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864131	1.00[ASN][1000 genomes]
rs3891250	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463020	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4505760	0.82[ASW][hapmap];0.85[MKK][hapmap]
rs4518182	1.00[ASN][1000 genomes]
rs58227539	1.00[ASN][1000 genomes]
rs60316402	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71602496	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73056602	1.00[ASN][1000 genomes]
rs73058406	1.00[ASN][1000 genomes]
rs7436737	1.00[CHD][hapmap];0.90[MKK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9991613	0.92[CEU][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs9992641	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS 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	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv878248	chr4:645300-685993	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv878249	chr4:649639-691026	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28583078	ZNF721	cis	parietal	SCAN
rs28583078	RP11-1191J2.2	cis	lung	GTEx
rs28583078	POLN	cis	parietal	SCAN
rs28583078	RP11-1191J2.2	cis	Thyroid	GTEx
rs28583078	RP11-1191J2.2	cis	Nerve Tibial	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:658000-664400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:658000-667000	Weak transcription	Small Intestine	intestine
3	chr4:658000-667400	Weak transcription	Aorta	Aorta
4	chr4:658200-659400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:658200-659400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr4:658200-660000	Enhancers	Brain Cingulate Gyrus	brain
7	chr4:658200-660400	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr4:658200-660600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:658200-660600	Enhancers	Brain Hippocampus Middle	brain
10	chr4:658200-664400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:658200-664400	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:658200-664400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:658200-664400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:658200-664600	Weak transcription	Pancreas	Pancrea
15	chr4:658200-664600	Weak transcription	HUVEC	blood vessel
16	chr4:658200-664800	Weak transcription	Gastric	stomach
17	chr4:658200-665000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:658200-666800	Weak transcription	Right Atrium	heart
19	chr4:658200-667000	Weak transcription	Stomach Mucosa	stomach
20	chr4:658200-667200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:658400-659400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr4:658400-659400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr4:658400-659400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr4:658400-659800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:658400-659800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr4:658400-660000	Enhancers	Brain Angular Gyrus	brain
27	chr4:658400-660200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr4:658400-660200	Enhancers	Brain Anterior Caudate	brain
29	chr4:658400-660400	Enhancers	Fetal Muscle Leg	muscle
30	chr4:658400-660800	Enhancers	Brain Substantia Nigra	brain
31	chr4:658400-662000	Enhancers	Fetal Muscle Trunk	muscle
32	chr4:658400-663600	Weak transcription	Fetal Stomach	stomach
33	chr4:658400-663800	Weak transcription	Primary T cells from cord blood	blood
34	chr4:658400-663800	Weak transcription	Brain Germinal Matrix	brain
35	chr4:658400-664400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:658400-664400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:658400-664400	Weak transcription	Liver	Liver
38	chr4:658400-664400	Weak transcription	Left Ventricle	heart
39	chr4:658400-664400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr4:658400-664400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr4:658400-664400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:658400-664400	Weak transcription	HMEC	breast
43	chr4:658400-664600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr4:658400-664600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:658400-664600	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:658400-664600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:658400-664600	Weak transcription	Fetal Brain Female	brain
48	chr4:658400-664600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:658400-664600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr4:658400-664600	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links