Variant report

Variant	rs12402888
Chromosome Location	chr1:160059748-160059749
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160057657..160060431-chr1:160187364..160189650,2	MCF-7	breast:
2	chr1:160054015..160055623-chr1:160058900..160060518,2	K562	blood:
3	chr1:160054542..160058051-chr1:160058705..160061578,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132716	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11265317	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265328	0.83[AFR][1000 genomes]
rs1131891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186675	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12092798	0.87[CEU][hapmap]
rs12401728	0.87[CEU][hapmap]
rs12401984	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12402134	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12408242	0.87[CEU][hapmap]
rs12408584	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12727520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17846705	0.83[AFR][1000 genomes]
rs1884998	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2295621	0.83[CEU][hapmap]
rs3747619	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761684	0.82[JPT][hapmap]
rs41265757	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4656879	0.82[JPT][hapmap]
rs55753565	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56187338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56211999	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61821993	0.81[EUR][1000 genomes]
rs61822013	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61822015	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs970365	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv520189	chr1:160011512-160095625	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1806746	chr1:160029416-160105927	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824420	chr1:160029416-160105927	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1843994	chr1:160029416-160105927	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv534066	chr1:160029416-160105986	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv1794281	chr1:160029416-160111565	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv1820784	chr1:160029416-160159395	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv534165	chr1:160029416-160187302	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160051400-160061600	Weak transcription	HepG2	liver
2	chr1:160052400-160060400	Weak transcription	Dnd41	blood
3	chr1:160053000-160065200	Weak transcription	Hela-S3	cervix
4	chr1:160053200-160062000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:160053600-160063200	Weak transcription	Small Intestine	intestine
6	chr1:160053800-160066000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:160054000-160066400	Weak transcription	NHDF-Ad	bronchial
8	chr1:160054200-160061400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:160054200-160063400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:160054400-160060200	Weak transcription	Right Ventricle	heart
11	chr1:160054400-160060400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:160054400-160060400	Weak transcription	NHEK	skin
13	chr1:160054400-160060600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:160054400-160061400	Weak transcription	Left Ventricle	heart
15	chr1:160054400-160064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:160054400-160065400	Weak transcription	Right Atrium	heart
17	chr1:160054400-160066000	Weak transcription	GM12878-XiMat	blood
18	chr1:160054400-160066200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:160054400-160066200	Weak transcription	HMEC	breast
20	chr1:160054400-160066600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:160054600-160060200	Weak transcription	Pancreas	Pancrea
22	chr1:160054600-160063000	Strong transcription	Thymus	Thymus
23	chr1:160054800-160062000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:160055600-160059800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:160055600-160060600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:160055600-160060600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:160055800-160060400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:160055800-160063000	Strong transcription	Fetal Intestine Small	intestine
29	chr1:160055800-160065400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:160055800-160066400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:160056000-160060200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:160056000-160060800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:160056000-160061200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:160056000-160061200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:160056000-160065400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:160056200-160060200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:160056200-160060400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:160056200-160060400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:160056200-160060600	Weak transcription	Aorta	Aorta
40	chr1:160056400-160060600	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:160056400-160063000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:160056400-160065200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:160056600-160062400	Strong transcription	Liver	Liver
44	chr1:160056600-160063000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr1:160056600-160063200	Strong transcription	Primary T cells from cord blood	blood
46	chr1:160056600-160065400	Genic enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:160056800-160060000	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:160056800-160061400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:160056800-160061800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:160056800-160065200	Strong transcription	Adipose Nuclei	Adipose

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