Variant report

Variant	rs1409367
Chromosome Location	chr1:153463451-153463452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153445167..153447773-chr1:153461159..153464090,2	MCF-7	breast:
2	chr1:153371450..153373306-chr1:153462974..153465949,3	MCF-7	breast:
3	chr1:153323483..153340048-chr1:153448254..153469845,61	MCF-7	breast:
4	chr1:153362845..153364948-chr1:153461555..153463988,2	MCF-7	breast:
5	chr1:153434339..153436072-chr1:153461738..153464674,2	MCF-7	breast:
6	chr1:153452726..153455263-chr1:153460858..153463511,2	MCF-7	breast:
7	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
8	chr1:153354527..153358677-chr1:153460629..153464225,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction
ENSG00000143546	Chromatin interaction
ENSG00000163218	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1359627	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1409368	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555886	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16835341	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16835343	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1853956	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1998844	0.85[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2026563	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2339694	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2986206	0.87[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2986210	0.85[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2986214	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006426	0.82[ASN][1000 genomes]
rs3006428	0.82[ASN][1000 genomes]
rs3006429	0.82[ASN][1000 genomes]
rs3006433	0.87[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs3006438	0.87[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3014831	0.82[ASN][1000 genomes]
rs3014832	0.81[ASN][1000 genomes]
rs3014835	0.83[ASN][1000 genomes]
rs3014836	0.86[ASN][1000 genomes]
rs3014838	0.86[ASN][1000 genomes]
rs3014839	0.87[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3014843	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3014845	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3014849	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3014851	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3125233	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587742	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6667320	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719081	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875501	0.83[ASN][1000 genomes]
rs9435988	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9633411	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
6	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153451000-153467400	Weak transcription	Ovary	ovary
2	chr1:153457200-153465800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:153459000-153467800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:153460600-153464400	Enhancers	Fetal Heart	heart
5	chr1:153461000-153464400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:153461000-153465000	Enhancers	Fetal Muscle Leg	muscle
7	chr1:153461200-153464000	Enhancers	Lung	lung
8	chr1:153461200-153464400	Enhancers	Fetal Muscle Trunk	muscle
9	chr1:153461200-153464400	Enhancers	Rectal Smooth Muscle	rectum
10	chr1:153461600-153463800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:153461600-153467600	Weak transcription	Psoas Muscle	Psoas
12	chr1:153462000-153463800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:153462000-153464400	Enhancers	Esophagus	oesophagus
14	chr1:153462200-153463800	Enhancers	NH-A	brain
15	chr1:153462200-153464000	Enhancers	Brain Angular Gyrus	brain
16	chr1:153462200-153464600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:153462200-153464600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:153462400-153464400	Enhancers	NHLF	lung
19	chr1:153462600-153463600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:153462600-153463600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:153462600-153463600	Enhancers	Brain Anterior Caudate	brain
22	chr1:153462600-153463600	Enhancers	Brain Cingulate Gyrus	brain
23	chr1:153462600-153463600	Enhancers	A549	lung
24	chr1:153462600-153463800	Flanking Active TSS	Hela-S3	cervix
25	chr1:153462600-153464200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:153462600-153464200	Enhancers	Adipose Nuclei	Adipose
27	chr1:153462600-153464200	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr1:153462600-153464400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:153462600-153464400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:153462600-153464400	Enhancers	Colon Smooth Muscle	Colon
31	chr1:153462800-153463600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:153462800-153463600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr1:153462800-153463800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:153462800-153463800	Enhancers	Fetal Stomach	stomach
35	chr1:153462800-153463800	Weak transcription	Left Ventricle	heart
36	chr1:153462800-153464000	Enhancers	Fetal Lung	lung
37	chr1:153462800-153464200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:153462800-153464200	Enhancers	Stomach Smooth Muscle	stomach
39	chr1:153462800-153479000	Weak transcription	Right Atrium	heart
40	chr1:153463000-153463600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:153463000-153463600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:153463000-153463600	Enhancers	Brain Hippocampus Middle	brain
43	chr1:153463000-153463600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr1:153463000-153463600	Enhancers	HSMMtube	muscle
45	chr1:153463000-153463600	Flanking Active TSS	Osteobl	bone
46	chr1:153463000-153464000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:153463000-153467600	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:153463000-153467600	Weak transcription	Right Ventricle	heart
49	chr1:153463200-153463600	Flanking Active TSS	HSMM	muscle
50	chr1:153463200-153464000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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