Variant report

Variant	rs28696717
Chromosome Location	chr1:153465563-153465564
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153371450..153373306-chr1:153462974..153465949,3	MCF-7	breast:
2	chr1:153323483..153340048-chr1:153448254..153469845,61	MCF-7	breast:
3	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
4	chr1:153440604..153442284-chr1:153463514..153465969,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction
ENSG00000163218	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12021612	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12022550	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12024114	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12025638	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12044034	0.83[ASN][1000 genomes]
rs12047203	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12047494	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16835332	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16835339	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2339695	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2986209	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3014848	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56009204	0.81[ASN][1000 genomes]
rs72708789	0.84[EUR][1000 genomes];0.91[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:38 , 50 per page) page: 1

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	chr1:153461600-153467600	Weak transcription	Psoas Muscle	Psoas
5	chr1:153462800-153479000	Weak transcription	Right Atrium	heart
6	chr1:153463000-153467600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:153463000-153467600	Weak transcription	Right Ventricle	heart
8	chr1:153463200-153467200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:153463400-153466800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:153463400-153467600	Weak transcription	Pancreas	Pancrea
11	chr1:153463600-153467000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:153463800-153467000	Weak transcription	Fetal Stomach	stomach
13	chr1:153464000-153467600	Weak transcription	Brain Angular Gyrus	brain
14	chr1:153464000-153469600	Weak transcription	Fetal Lung	lung
15	chr1:153464200-153466000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:153464200-153467600	Weak transcription	Adipose Nuclei	Adipose
17	chr1:153464400-153465800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:153464400-153465800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:153464400-153465800	Weak transcription	Aorta	Aorta
20	chr1:153464400-153465800	Weak transcription	Fetal Heart	heart
21	chr1:153464400-153465800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:153464400-153466000	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:153464400-153467200	Weak transcription	HSMM	muscle
24	chr1:153464400-153467600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:153464400-153467600	Weak transcription	Esophagus	oesophagus
26	chr1:153464400-153467600	Weak transcription	Fetal Thymus	thymus
27	chr1:153464400-153467600	Weak transcription	Left Ventricle	heart
28	chr1:153464400-153467600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:153464400-153467600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:153464400-153471400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:153464600-153465600	Weak transcription	Placenta	Placenta
32	chr1:153465000-153467200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:153465000-153467600	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:153465000-153467600	Enhancers	HMEC	breast
35	chr1:153465200-153466400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:153465400-153466200	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr1:153465400-153466400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:153465400-153466600	Enhancers	NHEK	skin

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