Variant report

Variant	rs6748632
Chromosome Location	chr2:110377855-110377856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:110376551..110378627-chr2:110403192..110405250,2	MCF-7	breast:
2	chr2:110370606..110375263-chr2:110377220..110379458,6	MCF-7	breast:
3	chr2:110373452..110379192-chr2:110379492..110383330,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186522	Chromatin interaction
ENSG00000198142	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11541143	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1434167	0.80[EUR][1000 genomes]
rs2018352	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2043462	0.88[ASN][1000 genomes]
rs2060402	0.84[ASN][1000 genomes]
rs2060403	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28544318	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28567471	0.81[ASN][1000 genomes]
rs28583991	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28615410	0.82[ASN][1000 genomes]
rs28622442	0.95[EUR][1000 genomes]
rs28728215	0.87[AMR][1000 genomes]
rs34557890	0.83[ASN][1000 genomes]
rs3829700	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3923006	0.85[AMR][1000 genomes]
rs4953760	0.83[ASN][1000 genomes]
rs4953784	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4953843	0.89[ASN][1000 genomes]
rs4953850	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56364682	0.83[ASN][1000 genomes]
rs56402128	0.83[ASN][1000 genomes]
rs6594037	0.86[ASN][1000 genomes]
rs6594049	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6723295	0.88[ASN][1000 genomes]
rs6726252	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6745809	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs747445	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7596172	0.86[ASN][1000 genomes]
rs892460	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs919941	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv829617	chr2:110359857-110380012	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6748632	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110374000-110378000	Weak transcription	HSMM	muscle
2	chr2:110374000-110379200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:110374600-110378000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:110374600-110380000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:110375600-110380800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:110376400-110379200	Weak transcription	Hela-S3	cervix
7	chr2:110377000-110378800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:110377200-110379600	Weak transcription	HepG2	liver
9	chr2:110377200-110380800	Weak transcription	Fetal Intestine Small	intestine
10	chr2:110377200-110387400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:110377600-110379800	Weak transcription	Liver	Liver
12	chr2:110377800-110378000	Enhancers	GM12878-XiMat	blood
13	chr2:110377800-110380800	Weak transcription	Fetal Intestine Large	intestine

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