Variant report

Variant	rs16862842
Chromosome Location	chr3:150484844-150484845
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	BHLHE40	chr3:150483775-150484925	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150482364..150486179-chr3:150581053..150584766,4	MCF-7	breast:
2	chr3:150433681..150449199-chr3:150473254..150487048,35	MCF-7	breast:

Variant related genes	Relation type
SIAH2	TF binding region
ENSG00000244668	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1373418	0.81[EUR][1000 genomes]
rs1444197	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1533711	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs16862837	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs1814463	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1814464	0.81[EUR][1000 genomes]
rs1838337	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1879420	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1879421	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs1915365	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2014279	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2018246	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2116684	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2120596	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34348847	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34771595	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3851356	1.00[CEU][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41354246	0.81[EUR][1000 genomes]
rs41372346	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41454348	1.00[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56840421	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57278175	0.93[EUR][1000 genomes]
rs57359526	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57869178	0.81[EUR][1000 genomes]
rs57965761	0.86[AMR][1000 genomes]
rs58403524	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58418105	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60092981	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60259684	0.81[EUR][1000 genomes]
rs60523415	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60538652	0.91[AMR][1000 genomes]
rs61628582	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6440696	0.81[EUR][1000 genomes]
rs6440697	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6440698	0.81[EUR][1000 genomes]
rs6769917	0.81[EUR][1000 genomes]
rs6777178	0.81[EUR][1000 genomes]
rs6788895	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs6789306	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs6795396	0.93[EUR][1000 genomes]
rs6803830	1.00[EUR][1000 genomes]
rs6805481	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs6806197	0.93[EUR][1000 genomes]
rs71764080	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72993403	0.86[EUR][1000 genomes]
rs73003787	0.93[EUR][1000 genomes]
rs73003792	0.81[EUR][1000 genomes]
rs73006998	0.85[EUR][1000 genomes]
rs73010941	0.81[EUR][1000 genomes]
rs73010947	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73010956	0.81[EUR][1000 genomes]
rs73010964	0.81[EUR][1000 genomes]
rs73010965	0.81[EUR][1000 genomes]
rs73010967	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73869297	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7615125	1.00[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs7615292	1.00[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs7617507	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs7628481	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628776	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7636866	1.00[CEU][hapmap];0.84[JPT][hapmap]

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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1820145	chr3:150478018-150487945	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150482000-150488200	Weak transcription	Left Ventricle	heart
2	chr3:150482000-150488200	Weak transcription	Ovary	ovary
3	chr3:150482000-150491600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:150482000-150491800	Weak transcription	Gastric	stomach
5	chr3:150482200-150485000	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:150482200-150485600	Weak transcription	Right Atrium	heart
7	chr3:150482600-150488000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:150482600-150488400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:150482600-150488400	Weak transcription	NHDF-Ad	bronchial
10	chr3:150482600-150488400	Weak transcription	Osteobl	bone
11	chr3:150482800-150488000	Weak transcription	Fetal Heart	heart
12	chr3:150482800-150488200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:150482800-150488400	Weak transcription	Placenta	Placenta
14	chr3:150482800-150488800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:150482800-150488800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:150482800-150488800	Weak transcription	Adipose Nuclei	Adipose
17	chr3:150482800-150492600	Weak transcription	Spleen	Spleen
18	chr3:150483000-150488000	Weak transcription	Liver	Liver
19	chr3:150483600-150485000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:150483800-150490800	Weak transcription	Stomach Mucosa	stomach
21	chr3:150484200-150485400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:150484200-150485800	Enhancers	HepG2	liver
23	chr3:150484200-150488400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:150484200-150498600	Weak transcription	Fetal Intestine Small	intestine
25	chr3:150484400-150485200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:150484400-150485200	Enhancers	GM12878-XiMat	blood
27	chr3:150484400-150488200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:150484600-150485000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:150484600-150485800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr3:150484800-150485200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:150484800-150485600	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr3:150484800-150488200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:150484800-150493800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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