Variant report

Variant	rs4727478
Chromosome Location	chr7:100752698-100752699
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100751112..100754051-chr7:100759784..100762309,3	MCF-7	breast:
2	chr7:100741507..100743688-chr7:100752212..100754188,2	K562	blood:
3	chr7:100752460..100757093-chr7:100759104..100763544,6	MCF-7	breast:
4	chr7:100751333..100754687-chr7:100808849..100811916,3	MCF-7	breast:
5	chr7:100752028..100753852-chr7:100804786..100807341,2	MCF-7	breast:
6	chr7:100751228..100753347-chr7:100760665..100763411,4	K562	blood:
7	chr7:100737701..100741221-chr7:100750993..100753482,3	MCF-7	breast:
8	chr7:100752507..100754161-chr7:100756602..100759066,2	MCF-7	breast:
9	chr7:100750619..100754326-chr7:100769826..100772467,4	MCF-7	breast:
10	chr7:100750302..100752925-chr7:100778093..100782237,4	MCF-7	breast:
11	chr7:100751173..100754073-chr7:100768865..100771330,2	MCF-7	breast:
12	chr7:100752598..100755404-chr7:100758782..100760396,2	K562	blood:
13	chr7:100747760..100750554-chr7:100750656..100752898,2	K562	blood:
14	chr7:100741837..100746865-chr7:100749791..100753773,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000106366	Chromatin interaction
ENSG00000128564	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12535610	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912	0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs13229117	0.87[ASN][1000 genomes]
rs36093166	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4524722	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4621721	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62483743	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62483746	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465783	0.80[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs6945281	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6948536	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6965671	0.80[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs6968929	0.85[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7801428	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031942	chr7:100606734-100788660	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1833777	chr7:100632790-100800131	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1033081	chr7:100669629-100771824	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats 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
4	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
6	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
7	nsv464649	chr7:100739682-100810983	Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv607972	chr7:100739682-100810983	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	esv2422376	chr7:100743485-101016471	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4727478	MGC72080	cis	parietal	SCAN
rs4727478	FBXO24	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100733600-100755400	Weak transcription	Aorta	Aorta
2	chr7:100747600-100755400	Weak transcription	NHLF	lung
3	chr7:100747600-100760400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr7:100747800-100760600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr7:100750000-100760200	Weak transcription	Hela-S3	cervix
6	chr7:100750800-100752800	Enhancers	GM12878-XiMat	blood
7	chr7:100750800-100753000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:100750800-100753400	Enhancers	NHDF-Ad	bronchial
9	chr7:100750800-100753600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr7:100750800-100753600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:100750800-100756600	Enhancers	HUVEC	blood vessel
12	chr7:100751000-100752800	Enhancers	Esophagus	oesophagus
13	chr7:100751000-100752800	Enhancers	Fetal Muscle Trunk	muscle
14	chr7:100751000-100752800	Flanking Active TSS	HepG2	liver
15	chr7:100751000-100753000	Enhancers	HSMM	muscle
16	chr7:100751000-100753400	Enhancers	Placenta	Placenta
17	chr7:100751200-100753400	Enhancers	Fetal Muscle Leg	muscle
18	chr7:100751600-100752800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:100751600-100752800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:100751600-100752800	Enhancers	Right Ventricle	heart
21	chr7:100751600-100752800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr7:100751600-100752800	Enhancers	HSMMtube	muscle
23	chr7:100751600-100752800	Enhancers	K562	blood
24	chr7:100751600-100753000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr7:100751600-100753000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
26	chr7:100751600-100753400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:100751600-100753400	Enhancers	HMEC	breast
28	chr7:100751800-100753000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr7:100751800-100753000	Enhancers	Lung	lung
30	chr7:100752000-100752800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr7:100752200-100752800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:100752200-100752800	Enhancers	Right Atrium	heart
33	chr7:100752200-100752800	Enhancers	Stomach Smooth Muscle	stomach
34	chr7:100752200-100753000	Enhancers	Fetal Thymus	thymus
35	chr7:100752200-100753200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:100752400-100753400	Enhancers	A549	lung
37	chr7:100752400-100753400	Enhancers	NHEK	skin
38	chr7:100752400-100753600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:100752400-100754600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:100752400-100754600	Weak transcription	Ovary	ovary
41	chr7:100752400-100755000	Weak transcription	Fetal Stomach	stomach
42	chr7:100752400-100757200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:100752400-100757400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:100752400-100757400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:100752400-100764600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:100752600-100752800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:100752600-100754600	Weak transcription	Adipose Nuclei	Adipose
48	chr7:100752600-100754600	Weak transcription	Left Ventricle	heart
49	chr7:100752600-100754800	Weak transcription	Spleen	Spleen
50	chr7:100752600-100755200	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links