Variant report

Variant	rs6726252
Chromosome Location	chr2:110374215-110374216
allele	A/C/G/T
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	POLR2A	chr2:110373655-110374649	IMR90	lung:	n/a	n/a
2	POLR2A	chr2:110369085-110379088	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:110372608-110374359	Hela-S3	cervix:	n/a	n/a
4	MYC	chr2:110374077-110374838	MCF10A-Er-Src	breast:	n/a	n/a
5	CHD1	chr2:110369172-110374773	IMR90	lung:	n/a	n/a
6	POLR2A	chr2:110369290-110378742	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr2:110374122-110375164	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:110373614..110376215-chr2:110402569..110405240,2	MCF-7	breast:
2	chr2:110373452..110379192-chr2:110379492..110383330,5	MCF-7	breast:
3	chr2:110372868..110375029-chr2:110390874..110393546,2	MCF-7	breast:

Variant related genes	Relation type
SEPT10	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11541143	0.80[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1434167	0.95[EUR][1000 genomes]
rs2018352	0.90[ASN][1000 genomes]
rs2043462	0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2060402	0.95[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2060403	0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs28544318	0.84[ASN][1000 genomes]
rs28567471	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28583991	0.82[ASN][1000 genomes]
rs28615410	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28728215	0.81[ASN][1000 genomes]
rs34557890	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3934873	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4312506	0.92[EUR][1000 genomes]
rs4953760	0.85[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4953784	0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4953843	0.90[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4953850	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56288075	0.94[EUR][1000 genomes]
rs56364682	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56402128	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6594037	0.85[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6594049	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705503	0.81[CHB][hapmap]
rs6723295	0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6745809	0.84[ASN][1000 genomes]
rs6748632	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs747445	0.89[ASN][1000 genomes]
rs7596172	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs892460	0.90[ASN][1000 genomes]
rs919941	0.80[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9330320	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9330324	0.85[AMR][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
rs6726252	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110369400-110374600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:110370000-110374800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:110370000-110375000	Active TSS	NHEK	skin
4	chr2:110372600-110374800	Enhancers	Fetal Heart	heart
5	chr2:110373000-110375800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:110373200-110374600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:110373200-110374600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:110373200-110375400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:110373400-110374400	Flanking Active TSS	A549	lung
10	chr2:110373400-110374600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:110373400-110374800	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr2:110373600-110374600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:110373600-110374600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:110373600-110374600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:110373600-110374800	Weak transcription	Pancreas	Pancrea
16	chr2:110373600-110375200	Weak transcription	Lung	lung
17	chr2:110373800-110374400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:110373800-110374400	Active TSS	HMEC	breast
19	chr2:110373800-110374600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:110373800-110374600	Active TSS	GM12878-XiMat	blood
21	chr2:110373800-110374800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr2:110373800-110374800	Enhancers	Colon Smooth Muscle	Colon
23	chr2:110373800-110374800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr2:110373800-110375200	Flanking Active TSS	Liver	Liver
25	chr2:110374000-110374400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:110374000-110374400	Enhancers	Adipose Nuclei	Adipose
27	chr2:110374000-110374400	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr2:110374000-110374400	Active TSS	Fetal Brain Male	brain
29	chr2:110374000-110374400	Flanking Active TSS	Fetal Kidney	kidney
30	chr2:110374000-110374600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
31	chr2:110374000-110374600	Enhancers	Fetal Lung	lung
32	chr2:110374000-110374600	Active TSS	Fetal Stomach	stomach
33	chr2:110374000-110374600	Active TSS	HepG2	liver
34	chr2:110374000-110374600	Active TSS	Osteobl	bone
35	chr2:110374000-110374800	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr2:110374000-110375000	Active TSS	NH-A	brain
37	chr2:110374000-110375200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:110374000-110375200	Weak transcription	Esophagus	oesophagus
39	chr2:110374000-110377200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:110374000-110378000	Weak transcription	HSMM	muscle
41	chr2:110374000-110379200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:110374200-110374400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
43	chr2:110374200-110374400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:110374200-110374400	Active TSS	Fetal Brain Female	brain
45	chr2:110374200-110374600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:110374200-110374600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:110374200-110374600	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr2:110374200-110374600	Enhancers	Duodenum Mucosa	Duodenum
49	chr2:110374200-110374600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr2:110374200-110374600	Enhancers	HUVEC	blood vessel

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