Variant report

Variant	rs12057602
Chromosome Location	chr1:169333329-169333330
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169331328..169334287-chr1:169334911..169337205,2	MCF-7	breast:
2	chr1:169324847..169326824-chr1:169332989..169335675,2	K562	blood:
3	chr1:169332852..169334456-chr1:169336922..169338977,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117475	Chromatin interaction
ENSG00000143156	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10800437	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1080266	0.90[CHB][hapmap]
rs1080267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11802143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11808938	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12081283	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12097151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123168	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12129979	0.89[CHB][hapmap]
rs12145969	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12564558	1.00[CEU][hapmap]
rs12741540	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12751062	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12751379	1.00[CEU][hapmap]
rs12753710	1.00[CEU][hapmap]
rs16862051	1.00[CEU][hapmap]
rs16862093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753297	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3753300	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4656181	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6427180	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6688038	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6688139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6703463	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7528751	1.00[CEU][hapmap]
rs9783117	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
3	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:169309400-169336400	Weak transcription	Ovary	ovary
5	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
8	chr1:169317200-169333800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:169317800-169333800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
11	chr1:169318200-169334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:169324600-169335800	Weak transcription	Primary T cells from cord blood	blood
13	chr1:169325600-169335800	Weak transcription	K562	blood
14	chr1:169326200-169334200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:169327200-169335800	Weak transcription	Small Intestine	intestine
16	chr1:169327200-169336200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:169330000-169336400	Weak transcription	Psoas Muscle	Psoas
18	chr1:169330800-169335800	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:169330800-169336400	Weak transcription	Right Ventricle	heart
20	chr1:169331400-169335800	Weak transcription	Fetal Intestine Large	intestine
21	chr1:169331600-169333400	Enhancers	Osteobl	bone
22	chr1:169331600-169335600	Enhancers	HMEC	breast
23	chr1:169331800-169333400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:169331800-169333400	Enhancers	HUVEC	blood vessel
25	chr1:169331800-169333600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:169331800-169335800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:169331800-169336200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:169332000-169333600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr1:169332000-169334400	Enhancers	NHEK	skin
30	chr1:169332000-169335800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:169332200-169333400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:169332200-169334200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:169332200-169336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:169332600-169333400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:169332800-169333400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:169332800-169333400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:169332800-169334600	Enhancers	Placenta	Placenta
38	chr1:169332800-169334800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:169332800-169336400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:169333000-169333600	Enhancers	GM12878-XiMat	blood
41	chr1:169333000-169334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:169333000-169334400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:169333000-169336000	Weak transcription	NHDF-Ad	bronchial
44	chr1:169333000-169336200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:169333000-169336200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:169333000-169336200	Weak transcription	Thymus	Thymus
47	chr1:169333200-169333600	Enhancers	NH-A	brain
48	chr1:169333200-169334200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:169333200-169334200	Weak transcription	Dnd41	blood
50	chr1:169333200-169334400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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