Variant report

Variant	rs3923006
Chromosome Location	chr2:110291087-110291088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:110287242..110289237-chr2:110289566..110292595,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10175432	0.94[ASN][1000 genomes]
rs11541143	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12998808	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2018352	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2043462	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs2060402	0.94[ASN][1000 genomes]
rs2060403	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28369323	0.82[CHB][hapmap]
rs28544318	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28567471	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28583991	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28615410	0.92[ASN][1000 genomes]
rs28728215	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34557890	0.95[ASN][1000 genomes]
rs3934873	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4953760	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953784	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953843	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[ASN][1000 genomes]
rs4953850	0.85[AMR][1000 genomes]
rs56364682	0.95[ASN][1000 genomes]
rs56402128	0.95[ASN][1000 genomes]
rs6594037	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[ASN][1000 genomes]
rs6594049	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs6723295	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.90[ASN][1000 genomes]
rs6726252	0.80[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs6745809	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6748632	0.85[AMR][1000 genomes]
rs747445	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7596172	0.92[ASN][1000 genomes]
rs767628	0.82[CHB][hapmap]
rs892460	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs892464	0.82[CHB][hapmap]
rs919941	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9330310	0.82[ASN][1000 genomes]
rs9330311	0.92[ASN][1000 genomes]
rs9330320	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330324	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9751601	0.81[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	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	nsv2874	chr2:110289373-110333621	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3923006	SEPT10	cis	parietal	SCAN
rs3923006	ACOXL	cis	cerebellum	SCAN
rs3923006	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110274000-110292800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:110281000-110292800	Weak transcription	Spleen	Spleen
3	chr2:110285000-110299200	Weak transcription	Aorta	Aorta
4	chr2:110287200-110293200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:110288000-110292600	Weak transcription	Right Ventricle	heart
6	chr2:110288000-110293200	Weak transcription	Ovary	ovary
7	chr2:110288000-110299000	Weak transcription	Esophagus	oesophagus
8	chr2:110288600-110293000	Weak transcription	Gastric	stomach
9	chr2:110288800-110292600	Weak transcription	Right Atrium	heart
10	chr2:110288800-110292800	Weak transcription	Placenta	Placenta
11	chr2:110288800-110293000	Weak transcription	Lung	lung
12	chr2:110289200-110292400	Weak transcription	Fetal Heart	heart
13	chr2:110290400-110291400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:110290600-110291400	Enhancers	Fetal Kidney	kidney
15	chr2:110290600-110291800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:110290600-110293400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:110290800-110291400	Bivalent Enhancer	HepG2	liver
18	chr2:110291000-110309400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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