Variant report

Variant	rs4555615
Chromosome Location	chr4:7939578-7939579
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	CHD1	chr4:7938516-7942221	IMR90	lung:	n/a	n/a
2	TCF12	chr4:7939530-7940047	A549	lung:	n/a	chr4:7939883-7939890
3	MAX	chr4:7939526-7940065	A549	lung:	n/a	n/a
4	NRF1	chr4:7939489-7939843	SK-N-SH	brain:	n/a	chr4:7939686-7939700
5	POLR2A	chr4:7939500-7942061	PANC-1	pancreas:	n/a	n/a
6	CTCF	chr4:7939500-7939650	HCPEpiC	choroid plexus:	n/a	n/a
7	POLR2A	chr4:7939405-7940717	PANC-1	pancreas:	n/a	n/a
8	CTCF	chr4:7939540-7939690	AG10803	skin:	n/a	n/a
9	POLR2A	chr4:7939516-7942080	HUVEC	blood vessel:	n/a	n/a
10	MAZ	chr4:7939417-7942102	IMR90	lung:	n/a	chr4:7940793-7940802
11	CTCF	chr4:7939500-7939650	HBMEC	blood vessel:	n/a	n/a
12	CTCF	chr4:7939520-7939670	HCM	heart:	n/a	n/a
13	MXI1	chr4:7939421-7942036	IMR90	lung:	n/a	n/a
14	CTCF	chr4:7939520-7939670	HRPEpiC	eye:	n/a	n/a
15	POLR2A	chr4:7939541-7942011	IMR90	lung:	n/a	n/a
16	MXI1	chr4:7939452-7942147	SK-N-SH	brain:	n/a	n/a
17	RAD21	chr4:7939529-7939877	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7799366..7802066-chr4:7938906..7941900,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	TF binding region
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12499560	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12505812	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2386048	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2386049	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2386050	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2386051	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2386053	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28711584	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2891924	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2891926	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4235266	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696685	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696686	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696687	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696824	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696829	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4696830	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4696832	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57868040	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58012905	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290603	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66806187	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7689238	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7931400-7939800	Weak transcription	Fetal Kidney	kidney
2	chr4:7931600-7939600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:7931600-7939600	Weak transcription	Ovary	ovary
4	chr4:7931600-7939600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:7931600-7939800	Weak transcription	Lung	lung
6	chr4:7931800-7939600	Weak transcription	Brain Angular Gyrus	brain
7	chr4:7932000-7939600	Weak transcription	Brain Anterior Caudate	brain
8	chr4:7932000-7939600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:7932000-7939600	Weak transcription	Left Ventricle	heart
10	chr4:7932000-7939600	Weak transcription	NHLF	lung
11	chr4:7932000-7939800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:7932000-7939800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:7932000-7939800	Weak transcription	Small Intestine	intestine
14	chr4:7932200-7939600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:7932200-7939600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:7932200-7939800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr4:7932200-7939800	Weak transcription	Pancreas	Pancrea
18	chr4:7932400-7939600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:7932800-7939600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr4:7935400-7939600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:7935600-7939600	Weak transcription	Aorta	Aorta
22	chr4:7935600-7939600	Enhancers	HSMMtube	muscle
23	chr4:7935800-7939600	Weak transcription	Placenta	Placenta
24	chr4:7936200-7939600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:7936200-7939800	Weak transcription	Right Ventricle	heart
26	chr4:7936400-7939600	Weak transcription	Fetal Intestine Small	intestine
27	chr4:7936400-7939600	Weak transcription	Stomach Mucosa	stomach
28	chr4:7936400-7939800	Weak transcription	Esophagus	oesophagus
29	chr4:7936600-7939600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:7936600-7939800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:7936600-7939800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:7936600-7939800	Weak transcription	Gastric	stomach
33	chr4:7937000-7939600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr4:7937200-7939600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:7937400-7939800	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr4:7937600-7939600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr4:7937800-7939600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:7937800-7941800	Active TSS	A549	lung
39	chr4:7938000-7939600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:7938000-7939600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:7938200-7941800	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr4:7938400-7939600	Enhancers	Fetal Brain Male	brain
43	chr4:7938600-7939600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:7938600-7939600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr4:7938600-7939600	Enhancers	Adipose Nuclei	Adipose
46	chr4:7938600-7940000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:7938800-7939600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:7938800-7939600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr4:7938800-7939600	Enhancers	Fetal Lung	lung
50	chr4:7938800-7939600	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links