Variant report

Variant	rs859005
Chromosome Location	chr1:158148599-158148600
allele	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	FOS	chr1:158148419-158148768	MCF10A-Er-Src	breast:	n/a	chr1:158148577-158148587 chr1:158148577-158148587 chr1:158148577-158148587
2	STAT3	chr1:158148479-158148808	MCF10A-Er-Src	breast:	n/a	chr1:158148651-158148659 chr1:158148649-158148660
3	FOS	chr1:158148417-158148808	MCF10A-Er-Src	breast:	n/a	chr1:158148577-158148587 chr1:158148577-158148587 chr1:158148577-158148587
4	STAT3	chr1:158148486-158148802	MCF10A-Er-Src	breast:	n/a	chr1:158148651-158148659 chr1:158148649-158148660
5	FOS	chr1:158148418-158148735	MCF10A-Er-Src	breast:	n/a	chr1:158148577-158148587 chr1:158148577-158148587 chr1:158148577-158148587
6	STAT3	chr1:158148445-158148841	MCF10A-Er-Src	breast:	n/a	chr1:158148651-158148659 chr1:158148649-158148660

Variant related genes	Relation type
CD1D	TF binding region
ELL2P1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10489821	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040592	0.91[CEU][hapmap]
rs12723141	0.95[JPT][hapmap]
rs1570699	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1633141	0.92[CEU][hapmap]
rs1633149	0.92[CEU][hapmap]
rs16839951	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1748383	0.92[CEU][hapmap]
rs1748387	0.92[CEU][hapmap]
rs1980757	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2269715	0.80[JPT][hapmap]
rs2518477	0.92[CEU][hapmap]
rs3021476	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3021478	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087213	0.82[EUR][1000 genomes]
rs3118165	0.92[CEU][hapmap]
rs368130	0.92[CEU][hapmap]
rs374513	0.92[CEU][hapmap]
rs377795	0.92[CEU][hapmap]
rs383688	0.92[CEU][hapmap]
rs384414	0.92[CEU][hapmap]
rs389495	0.91[CEU][hapmap]
rs393304	0.84[CEU][hapmap]
rs401904	0.92[CEU][hapmap]
rs402699	0.92[CEU][hapmap]
rs407309	0.92[CEU][hapmap]
rs413557	0.92[CEU][hapmap]
rs434570	0.92[CEU][hapmap]
rs440862	0.92[CEU][hapmap]
rs448005	0.92[CEU][hapmap]
rs448556	0.92[CEU][hapmap]
rs449838	0.92[CEU][hapmap]
rs594364	0.92[CEU][hapmap]
rs607948	0.92[CEU][hapmap]
rs623215	0.92[CEU][hapmap]
rs6692064	0.92[EUR][1000 genomes]
rs6692133	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs691077	0.83[CEU][hapmap]
rs691175	0.92[CEU][hapmap]
rs691551	0.92[CEU][hapmap]
rs72711995	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72711999	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7530662	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs7548147	1.00[JPT][hapmap]
rs7556487	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859001	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859002	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs859008	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859009	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859010	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs859011	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859013	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158143800-158149000	Weak transcription	Small Intestine	intestine
2	chr1:158147000-158150000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr1:158147000-158150400	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr1:158147400-158148600	Active TSS	Duodenum Mucosa	Duodenum
5	chr1:158147800-158149400	Weak transcription	Pancreas	Pancrea
6	chr1:158147800-158150400	Weak transcription	Left Ventricle	heart
7	chr1:158147800-158150600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr1:158148000-158149400	Weak transcription	Right Ventricle	heart
9	chr1:158148000-158149400	Weak transcription	Thymus	Thymus
10	chr1:158148000-158150400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:158148000-158150400	Weak transcription	Esophagus	oesophagus
12	chr1:158148000-158150600	Weak transcription	Ovary	ovary
13	chr1:158148200-158148600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:158148200-158148600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:158148200-158149000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:158148200-158149200	Weak transcription	Fetal Intestine Large	intestine
17	chr1:158148200-158149200	Weak transcription	Right Atrium	heart
18	chr1:158148200-158149600	Weak transcription	Fetal Heart	heart
19	chr1:158148200-158150000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:158148200-158150200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:158148200-158150200	Enhancers	Fetal Kidney	kidney
22	chr1:158148200-158150200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:158148200-158150600	Weak transcription	Aorta	Aorta
24	chr1:158148400-158148600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:158148400-158148600	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:158148400-158148800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:158148400-158148800	Flanking Active TSS	Liver	Liver
28	chr1:158148400-158148800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:158148400-158149200	Enhancers	Primary B cells from cord blood	blood
30	chr1:158148400-158149200	Weak transcription	Psoas Muscle	Psoas
31	chr1:158148400-158149200	Enhancers	GM12878-XiMat	blood
32	chr1:158148400-158149400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:158148400-158149400	Enhancers	Fetal Intestine Small	intestine
34	chr1:158148400-158149600	Weak transcription	Primary T cells from cord blood	blood
35	chr1:158148400-158149800	Weak transcription	HMEC	breast
36	chr1:158148400-158149800	Weak transcription	NHEK	skin
37	chr1:158148400-158150000	Enhancers	Primary B cells from peripheral blood	blood
38	chr1:158148400-158150200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr1:158148400-158150400	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:158148400-158150400	Weak transcription	Colonic Mucosa	Colon

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