Variant report

Variant	rs2879553
Chromosome Location	chr1:153466377-153466378
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153466147..153468573-chr1:153470167..153472287,2	MCF-7	breast:
2	chr1:153324719..153325873-chr1:153465623..153466614,3	MCF-7	breast:
3	chr1:153323483..153340048-chr1:153448254..153469845,61	MCF-7	breast:
4	chr1:153359777..153361314-chr1:153466006..153468984,2	MCF-7	breast:
5	chr1:153366171..153367906-chr1:153465906..153468901,2	MCF-7	breast:
6	chr1:153440789..153442801-chr1:153466066..153467903,2	MCF-7	breast:
7	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
8	chr1:153437206..153440694-chr1:153466029..153468031,4	MCF-7	breast:
9	chr1:153325982..153326575-chr1:153465866..153466749,2	MCF-7	breast:
10	chr1:153324699..153327134-chr1:153466308..153468062,18	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163218	Chromatin interaction
ENSG00000163220	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs16835366	0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16835368	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16835382	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs16835393	0.90[JPT][hapmap]
rs17695220	0.90[JPT][hapmap]
rs1887039	0.90[JPT][hapmap]
rs28676601	0.83[ASN][1000 genomes]
rs28707433	0.83[ASN][1000 genomes]
rs4272569	0.90[JPT][hapmap]
rs4430277	0.90[JPT][hapmap]
rs4845351	0.90[JPT][hapmap]
rs4845352	0.88[JPT][hapmap]
rs4845548	0.83[ASN][1000 genomes]
rs4845549	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap]
rs4845550	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs4845552	0.90[JPT][hapmap]
rs4845554	0.90[JPT][hapmap]
rs6587743	0.90[JPT][hapmap]
rs6660055	0.83[ASN][1000 genomes]
rs6672390	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6679509	0.83[ASN][1000 genomes]
rs6684970	0.90[JPT][hapmap]
rs7518306	0.90[JPT][hapmap]
rs9436094	0.83[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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2879553	PSMB4	cis	parietal	SCAN
rs2879553	LCE2C	cis	parietal	SCAN
rs2879553	PSMD4	cis	parietal	SCAN
rs2879553	RN7SL44P	cis	Nerve Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153451000-153467400	Weak transcription	Ovary	ovary
2	chr1:153459000-153467800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:153461600-153467600	Weak transcription	Psoas Muscle	Psoas
4	chr1:153462800-153479000	Weak transcription	Right Atrium	heart
5	chr1:153463000-153467600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:153463000-153467600	Weak transcription	Right Ventricle	heart
7	chr1:153463200-153467200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:153463400-153466800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:153463400-153467600	Weak transcription	Pancreas	Pancrea
10	chr1:153463600-153467000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:153463800-153467000	Weak transcription	Fetal Stomach	stomach
12	chr1:153464000-153467600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:153464000-153469600	Weak transcription	Fetal Lung	lung
14	chr1:153464200-153467600	Weak transcription	Adipose Nuclei	Adipose
15	chr1:153464400-153467200	Weak transcription	HSMM	muscle
16	chr1:153464400-153467600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:153464400-153467600	Weak transcription	Esophagus	oesophagus
18	chr1:153464400-153467600	Weak transcription	Fetal Thymus	thymus
19	chr1:153464400-153467600	Weak transcription	Left Ventricle	heart
20	chr1:153464400-153467600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:153464400-153467600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:153464400-153471400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:153465000-153467200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:153465000-153467600	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:153465000-153467600	Enhancers	HMEC	breast
26	chr1:153465200-153466400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:153465400-153466400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:153465400-153466600	Enhancers	NHEK	skin
29	chr1:153465800-153466400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr1:153465800-153466800	Enhancers	Rectal Smooth Muscle	rectum
31	chr1:153465800-153468600	Enhancers	Fetal Heart	heart
32	chr1:153466000-153466400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:153466000-153466400	Enhancers	Brain Hippocampus Middle	brain
34	chr1:153466000-153466600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:153466000-153467600	Weak transcription	Placenta	Placenta
36	chr1:153466000-153467800	Enhancers	Colon Smooth Muscle	Colon
37	chr1:153466000-153467800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr1:153466200-153467000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:153466200-153467400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:153466200-153471200	Weak transcription	Aorta	Aorta

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