Variant report

Variant	rs12486998
Chromosome Location	chr3:161136791-161136792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
2	chr3:160973929..160975707-chr3:161135693..161137534,2	MCF-7	breast:
3	chr15:66795099..66797100-chr3:161134725..161136811,2	MCF-7	breast:
4	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
5	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:
6	chr3:160938218..160944428-chr3:161134456..161142008,22	MCF-7	breast:
7	chr3:161136644..161139076-chr3:161160623..161163367,2	MCF-7	breast:
8	chr3:160677412..160680256-chr3:161134462..161137137,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000200623	Chromatin interaction
ENSG00000199673	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1017799	0.89[JPT][hapmap]
rs12486111	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12487002	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12488127	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12490149	1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap]
rs12491623	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12494520	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13319558	0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs13319771	0.88[JPT][hapmap]
rs1450518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2035499	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2306209	1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs4352387	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs4468992	0.89[JPT][hapmap]
rs56839556	0.94[ASN][1000 genomes]
rs58851337	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58892449	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59193340	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59368066	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6441375	1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes]
rs6775446	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs6775931	0.89[JPT][hapmap]
rs6781086	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6782415	0.89[JPT][hapmap]
rs6782518	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs6785714	0.82[JPT][hapmap]
rs6787697	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6793980	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6795310	0.84[YRI][hapmap]
rs73878309	0.85[AMR][1000 genomes]
rs73878323	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73878329	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7614130	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7626773	0.89[JPT][hapmap]
rs7629841	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7634299	0.89[JPT][hapmap]
rs7651924	0.89[JPT][hapmap];0.82[AMR][1000 genomes]
rs9819793	0.86[JPT][hapmap]
rs9822705	0.85[AMR][1000 genomes]
rs9822916	0.88[JPT][hapmap]
rs9824805	0.89[JPT][hapmap]
rs9835530	0.89[JPT][hapmap]
rs9847842	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs9851699	0.82[AMR][1000 genomes]
rs9855572	0.82[AMR][1000 genomes]
rs9859641	0.88[JPT][hapmap]
rs9860980	0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs9862867	0.89[JPT][hapmap]
rs9877309	0.84[JPT][hapmap]
rs9880536	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161125600-161137000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:161131600-161140000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:161134000-161138400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:161134200-161137400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:161134400-161137200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:161134400-161137400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:161134400-161137400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:161134400-161138400	Weak transcription	Fetal Lung	lung
9	chr3:161134400-161138600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:161134400-161139800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:161134400-161141200	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:161134400-161145200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:161134400-161148200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:161134600-161137000	Weak transcription	Aorta	Aorta
15	chr3:161134600-161137400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:161134600-161137800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:161134600-161138000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:161134600-161138000	Weak transcription	Liver	Liver
19	chr3:161134600-161138000	Weak transcription	Stomach Mucosa	stomach
20	chr3:161134600-161138000	Weak transcription	A549	lung
21	chr3:161134600-161138200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:161134600-161138200	Weak transcription	NHEK	skin
23	chr3:161134600-161138600	Weak transcription	HUVEC	blood vessel
24	chr3:161134600-161138600	Weak transcription	NH-A	brain
25	chr3:161134600-161138600	Weak transcription	NHLF	lung
26	chr3:161134600-161138800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:161134600-161138800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:161134600-161140000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:161134800-161138000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:161135600-161137400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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