Variant report

Variant	rs7686909
Chromosome Location	chr4:174257693-174257694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:174253089-174257840	PBDE	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:174088355..174091772-chr4:174254077..174258410,8	K562	blood:
2	chr4:174252933..174259053-chr4:174284716..174299463,25	MCF-7	breast:
3	chr4:174088713..174091772-chr4:174254390..174258410,4	K562	blood:
4	chr4:174256552..174259513-chr4:174261559..174263260,2	MCF-7	breast:
5	chr4:174254894..174256484-chr4:174257318..174259644,2	MCF-7	breast:
6	chr4:174245727..174260507-chr4:174283013..174295498,65	K562	blood:
7	chr4:174248778..174262653-chr4:174278408..174298501,82	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GALNT7-1	chr4:174257459-174258084	NONHSAT099233

No data

Variant related genes	Relation type
HMGB2	TF binding region
ENSG00000245213	Chromatin interaction
ENSG00000109586	Chromatin interaction
ENSG00000164105	Chromatin interaction
ENSG00000164104	Chromatin interaction
ENSG00000272870	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10471199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10520255	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs11132982	0.86[ASN][1000 genomes]
rs11722807	0.88[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs11726679	0.88[ASN][1000 genomes]
rs11728029	0.88[ASN][1000 genomes]
rs11729778	0.88[ASN][1000 genomes]
rs11731057	0.88[ASN][1000 genomes]
rs11731262	0.88[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs11734517	0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs11736050	0.88[ASN][1000 genomes]
rs13151627	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs1481120	0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs3733476	0.89[ASN][1000 genomes]
rs3775590	0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs3775591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4695829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56159092	0.88[ASN][1000 genomes]
rs58185783	0.88[ASN][1000 genomes]
rs58612091	0.86[ASN][1000 genomes]
rs61241252	0.88[ASN][1000 genomes]
rs61470087	0.88[ASN][1000 genomes]
rs6821844	0.88[ASN][1000 genomes]
rs6822924	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs6842693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73001510	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73001512	0.82[ASN][1000 genomes]
rs73003342	0.88[ASN][1000 genomes]
rs73003349	0.86[ASN][1000 genomes]
rs73003362	0.88[ASN][1000 genomes]
rs73003376	0.86[ASN][1000 genomes]
rs73005346	0.86[ASN][1000 genomes]
rs73005353	0.86[ASN][1000 genomes]
rs73005356	0.88[ASN][1000 genomes]
rs73005357	0.86[ASN][1000 genomes]
rs73005363	0.89[ASN][1000 genomes]
rs7664847	0.88[CHB][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs7665469	0.88[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs7668435	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7672055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv966552	chr4:174248506-174259305	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174254400-174257800	Active TSS	Thymus	Thymus
2	chr4:174254600-174257800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:174256600-174258000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:174256600-174258000	Flanking Active TSS	Dnd41	blood
5	chr4:174256800-174280400	Weak transcription	Aorta	Aorta
6	chr4:174257000-174257800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:174257000-174258000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:174257000-174258000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:174257000-174258000	Enhancers	Osteobl	bone
10	chr4:174257000-174258200	Enhancers	Hela-S3	cervix
11	chr4:174257000-174258400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:174257000-174258800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:174257000-174259000	Enhancers	NHDF-Ad	bronchial
14	chr4:174257000-174259200	Enhancers	Fetal Heart	heart
15	chr4:174257000-174261800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:174257000-174264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:174257000-174264400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:174257200-174257800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:174257200-174257800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:174257200-174257800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:174257200-174257800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:174257200-174257800	Enhancers	Fetal Lung	lung
23	chr4:174257200-174257800	Enhancers	HMEC	breast
24	chr4:174257200-174257800	Enhancers	NHEK	skin
25	chr4:174257200-174258000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:174257200-174258000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:174257200-174258000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:174257200-174258000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr4:174257200-174258000	Flanking Active TSS	GM12878-XiMat	blood
30	chr4:174257200-174258000	Enhancers	HepG2	liver
31	chr4:174257200-174258600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:174257200-174258800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:174257200-174264400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:174257400-174257800	Active TSS	Brain Germinal Matrix	brain
35	chr4:174257400-174257800	Flanking Active TSS	NHLF	lung
36	chr4:174257400-174258000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:174257400-174258000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
38	chr4:174257400-174258600	Weak transcription	HSMM	muscle
39	chr4:174257600-174257800	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr4:174257600-174257800	Enhancers	Fetal Intestine Small	intestine
41	chr4:174257600-174257800	Enhancers	A549	lung
42	chr4:174257600-174258000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:174257600-174258000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:174257600-174258000	Flanking Active TSS	K562	blood
45	chr4:174257600-174258600	Weak transcription	Fetal Thymus	thymus
46	chr4:174257600-174262000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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