Variant report

Variant	rs524166
Chromosome Location	chr1:179882450-179882451
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179849629..179853338-chr1:179880600..179883588,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1148813	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1148814	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1148816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1281409	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1281414	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1281415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1281419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1281425	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1281431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1290274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1295972	0.94[EUR][1000 genomes]
rs1299683	0.89[EUR][1000 genomes]
rs1299685	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17370666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1758143	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2501605	0.88[AFR][1000 genomes]
rs2762857	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2777907	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777910	0.85[YRI][hapmap]
rs2777916	0.89[EUR][1000 genomes]
rs2794584	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476280	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555755	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs576723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585355	0.85[YRI][hapmap]
rs627897	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651455	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs683812	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
2	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
6	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
7	chr1:179857600-179886800	Weak transcription	Psoas Muscle	Psoas
8	chr1:179860200-179890200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:179861200-179886600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:179861600-179886600	Weak transcription	Pancreas	Pancrea
11	chr1:179867200-179886600	Weak transcription	Small Intestine	intestine
12	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
13	chr1:179868200-179891600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr1:179868200-179891800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:179868400-179888800	Strong transcription	Adipose Nuclei	Adipose
16	chr1:179868400-179890600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:179868400-179890800	Strong transcription	Dnd41	blood
18	chr1:179868600-179891600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:179868600-179892000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:179868800-179889000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:179868800-179889200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:179868800-179889600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:179869000-179888200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:179869200-179885600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:179869200-179891600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:179869400-179889600	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:179869400-179891400	Strong transcription	Liver	Liver
28	chr1:179870000-179890400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:179871200-179891000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:179872000-179886600	Weak transcription	Brain Angular Gyrus	brain
31	chr1:179873200-179882600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:179873400-179884600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:179873400-179891400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:179873600-179886400	Weak transcription	HepG2	liver
35	chr1:179874000-179886600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:179874200-179886600	Weak transcription	Fetal Brain Female	brain
37	chr1:179874400-179886800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:179874600-179886000	Weak transcription	Thymus	Thymus
39	chr1:179875200-179891800	Strong transcription	Primary B cells from cord blood	blood
40	chr1:179875600-179882600	Weak transcription	A549	lung
41	chr1:179876000-179891200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:179876800-179883600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:179877000-179888600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:179877000-179891600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:179877200-179888800	Strong transcription	Placenta	Placenta
46	chr1:179877200-179889200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:179877800-179886800	Weak transcription	NHLF	lung
48	chr1:179878000-179886800	Weak transcription	Fetal Kidney	kidney
49	chr1:179878200-179884400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:179878200-179886600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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