Variant report

Variant	rs12568487
Chromosome Location	chr1:212626163-212626164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212611206..212613997-chr1:212623720..212626273,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11577176	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11578276	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12058471	1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12058803	0.83[AMR][1000 genomes]
rs12084711	0.83[AMR][1000 genomes]
rs12096385	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12568314	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292480	0.89[CHB][hapmap]
rs634296	0.88[ASN][1000 genomes]
rs6657001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73088527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74138155	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74140013	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7520772	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7520878	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7542213	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553792	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers 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
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv873157	chr1:212610755-212640982	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv873158	chr1:212610755-212646225	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv873159	chr1:212610755-212669475	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212607400-212629200	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr1:212607800-212629400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:212608000-212627000	Weak transcription	HepG2	liver
4	chr1:212614400-212626200	Weak transcription	Pancreas	Pancrea
5	chr1:212614400-212629200	Weak transcription	GM12878-XiMat	blood
6	chr1:212614400-212636800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:212618400-212627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:212619400-212627000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:212619600-212626400	Weak transcription	Spleen	Spleen
10	chr1:212619600-212629000	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:212619600-212629000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:212619600-212629000	Weak transcription	K562	blood
13	chr1:212619600-212629200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:212619600-212636800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:212619800-212629000	Weak transcription	A549	lung
16	chr1:212619800-212629200	Weak transcription	Primary T cells from cord blood	blood
17	chr1:212619800-212629200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr1:212620000-212626200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:212620000-212631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:212620200-212629200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:212620200-212629200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:212620200-212631400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:212620600-212626200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:212620800-212626400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:212620800-212629000	Weak transcription	Dnd41	blood
26	chr1:212620800-212629200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:212620800-212629200	Weak transcription	Fetal Intestine Large	intestine
28	chr1:212621400-212626200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:212621400-212626600	Weak transcription	Placenta	Placenta
30	chr1:212621400-212626600	Weak transcription	Lung	lung
31	chr1:212622400-212626800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:212622400-212627200	Enhancers	Brain Anterior Caudate	brain
33	chr1:212622400-212628000	Enhancers	Brain Cingulate Gyrus	brain
34	chr1:212622400-212628000	Enhancers	Brain Hippocampus Middle	brain
35	chr1:212622400-212628600	Enhancers	Fetal Muscle Trunk	muscle
36	chr1:212622400-212631000	Enhancers	Fetal Muscle Leg	muscle
37	chr1:212622800-212629400	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:212623000-212629400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:212623400-212627200	Enhancers	HSMMtube	muscle
40	chr1:212623600-212627000	Enhancers	Brain Substantia Nigra	brain
41	chr1:212623600-212627400	Enhancers	Left Ventricle	heart
42	chr1:212624400-212629200	Weak transcription	Fetal Thymus	thymus
43	chr1:212624800-212630000	Weak transcription	Esophagus	oesophagus
44	chr1:212625200-212627000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:212625200-212627400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:212625400-212627400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:212625400-212627400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:212625600-212626800	Enhancers	Fetal Heart	heart
49	chr1:212625600-212626800	Enhancers	Ovary	ovary
50	chr1:212625600-212627000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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