Variant report

Variant	rs12502667
Chromosome Location	chr4:148648861-148648862
allele	C/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	JUND	chr4:148648518-148649182	HCT-116	colon:	n/a	chr4:148648789-148648796 chr4:148648788-148648797 chr4:148648787-148648797 chr4:148648787-148648796
2	FOSL1	chr4:148648639-148649152	HCT-116	colon:	n/a	chr4:148648789-148648796 chr4:148648788-148648797 chr4:148648787-148648797 chr4:148648787-148648796
3	FOSL1	chr4:148648482-148649105	HCT-116	colon:	n/a	chr4:148648789-148648796 chr4:148648788-148648797 chr4:148648787-148648797 chr4:148648787-148648796
4	STAT3	chr4:148648614-148648898	MCF10A-Er-Src	breast:	n/a	chr4:148648788-148648797
5	POLR2A	chr4:148648605-148648930	HCT-116	colon:	n/a	n/a
6	STAT3	chr4:148648653-148648965	MCF10A-Er-Src	breast:	n/a	chr4:148648788-148648797
7	FOS	chr4:148648561-148648972	MCF10A-Er-Src	breast:	n/a	chr4:148648789-148648796 chr4:148648788-148648797 chr4:148648787-148648797 chr4:148648787-148648796
8	FOS	chr4:148648586-148648961	MCF10A-Er-Src	breast:	n/a	chr4:148648789-148648796 chr4:148648788-148648797 chr4:148648787-148648797 chr4:148648787-148648796
9	FOS	chr4:148648562-148649023	MCF10A-Er-Src	breast:	n/a	chr4:148648789-148648796 chr4:148648788-148648797 chr4:148648787-148648797 chr4:148648787-148648796
10	FOS	chr4:148648562-148648974	MCF10A-Er-Src	breast:	n/a	chr4:148648789-148648796 chr4:148648788-148648797 chr4:148648787-148648797 chr4:148648787-148648796

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148648744..148650659-chr4:148651832..148653944,2	MCF-7	breast:
2	chr4:148644588..148650740-chr4:148651237..148656325,11	MCF-7	breast:

Variant related genes	Relation type
ARHGAP10	TF binding region
ENSG00000071205	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10776520	1.00[CEU][hapmap]
rs11099667	0.84[ASN][1000 genomes]
rs11099669	0.86[AMR][1000 genomes]
rs11725260	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11726957	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11729081	0.86[MEX][hapmap];0.80[AMR][1000 genomes]
rs12640660	1.00[MEX][hapmap]
rs12645249	0.86[MEX][hapmap];0.80[AMR][1000 genomes]
rs12648074	0.80[AMR][1000 genomes]
rs13109759	0.81[ASN][1000 genomes]
rs13119467	0.85[CEU][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs13128620	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13134018	0.84[AMR][1000 genomes]
rs13144139	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1969102	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2055551	0.86[AMR][1000 genomes]
rs2118036	0.86[MEX][hapmap]
rs28505821	0.82[EUR][1000 genomes]
rs36052332	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4490438	0.81[EUR][1000 genomes]
rs4835093	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4835446	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4835448	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56224422	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6535556	0.84[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6535558	0.86[AMR][1000 genomes]
rs6535559	0.86[AMR][1000 genomes]
rs6535561	0.80[AMR][1000 genomes]
rs6822971	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs6827786	0.85[AMR][1000 genomes]
rs6828600	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6836509	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6839987	0.86[AMR][1000 genomes]
rs6845560	0.86[AMR][1000 genomes]
rs7661297	1.00[CEU][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs7666807	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7669809	0.83[EUR][1000 genomes]
rs7673234	0.86[AMR][1000 genomes]
rs7673606	0.86[AMR][1000 genomes]
rs905606	0.82[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9332471	1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs964170	0.86[MEX][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148644800-148652400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:148645000-148652000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:148645000-148652200	Weak transcription	Fetal Kidney	kidney
4	chr4:148645000-148652400	Weak transcription	Liver	Liver
5	chr4:148646000-148652200	Weak transcription	Adipose Nuclei	Adipose
6	chr4:148646200-148651600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:148646200-148652200	Weak transcription	GM12878-XiMat	blood
8	chr4:148646400-148651400	Weak transcription	HepG2	liver
9	chr4:148646400-148652400	Weak transcription	A549	lung
10	chr4:148647600-148649200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:148647600-148649600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:148648000-148649200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:148648200-148649400	Enhancers	HMEC	breast
14	chr4:148648200-148649400	Enhancers	NHEK	skin
15	chr4:148648400-148649000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:148648400-148649200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:148648400-148649200	Enhancers	NHDF-Ad	bronchial
18	chr4:148648600-148652200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:148648800-148649000	Enhancers	Placenta Amnion	Placenta Amnion

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