Variant report

Variant	rs4651208
Chromosome Location	chr1:184442054-184442055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184434578..184437265-chr1:184439841..184442761,2	MCF-7	breast:
2	chr1:184427992..184429921-chr1:184441519..184443422,2	MCF-7	breast:
3	chr1:184440449..184442376-chr1:184450326..184452605,2	MCF-7	breast:
4	chr1:184355623..184357608-chr1:184441118..184443754,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271387	Chromatin interaction
ENSG00000116667	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1007224	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs10737253	0.97[ASN][1000 genomes]
rs10797971	0.91[ASN][1000 genomes]
rs10797972	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.87[ASN][1000 genomes]
rs10911606	0.82[CHB][hapmap]
rs11588922	0.84[ASN][1000 genomes]
rs12125349	0.80[ASN][1000 genomes]
rs12127674	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1339563	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1339564	0.83[ASN][1000 genomes]
rs1339565	0.80[ASN][1000 genomes]
rs1339566	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs1569842	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1884200	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2001270	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs2038307	0.89[ASN][1000 genomes]
rs2038308	0.82[CHB][hapmap];0.82[CHD][hapmap];0.85[MKK][hapmap]
rs2180073	0.83[CHB][hapmap]
rs2180077	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2207528	0.97[ASN][1000 genomes]
rs2378888	0.85[ASN][1000 genomes]
rs2890015	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4650667	0.83[ASN][1000 genomes]
rs4651210	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4651211	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4651216	0.87[ASN][1000 genomes]
rs4651217	0.80[ASN][1000 genomes]
rs55729410	0.97[ASN][1000 genomes]
rs6661707	0.94[ASN][1000 genomes]
rs6666704	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7517518	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7533466	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7544240	0.80[ASN][1000 genomes]
rs9633308	0.82[GIH][hapmap]
rs9970984	0.83[ASN][1000 genomes]
rs9970990	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4651208	ARPC5	cis	parietal	SCAN
rs4651208	ABL2	cis	parietal	SCAN
rs4651208	TDRD5	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184425400-184442200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:184427400-184443800	Weak transcription	Esophagus	oesophagus
3	chr1:184427400-184444000	Weak transcription	Lung	lung
4	chr1:184427400-184448400	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:184429000-184454800	Weak transcription	Aorta	Aorta
6	chr1:184429400-184449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:184429600-184442200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:184430600-184444000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:184430600-184449800	Weak transcription	Right Ventricle	heart
10	chr1:184430600-184450000	Weak transcription	Fetal Stomach	stomach
11	chr1:184431400-184446400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:184431800-184447600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:184432000-184443400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:184433200-184442200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:184433600-184449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:184433800-184443600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:184436800-184442400	Weak transcription	Left Ventricle	heart
18	chr1:184436800-184442400	Weak transcription	Ovary	ovary
19	chr1:184436800-184444000	Weak transcription	Pancreas	Pancrea
20	chr1:184438000-184450600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:184439200-184453600	Weak transcription	Fetal Brain Female	brain
22	chr1:184440600-184445800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:184440800-184442600	Enhancers	Fetal Heart	heart
24	chr1:184440800-184446200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:184441000-184442200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:184441000-184442200	Weak transcription	Psoas Muscle	Psoas
27	chr1:184441000-184443000	Enhancers	Fetal Brain Male	brain
28	chr1:184441000-184443800	Weak transcription	Right Atrium	heart
29	chr1:184441000-184445000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:184441000-184452000	Weak transcription	Colonic Mucosa	Colon
31	chr1:184441600-184443800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:184441600-184443800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:184441800-184442800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:184441800-184442800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:184441800-184447400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:184442000-184442600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:184442000-184442600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:184442000-184442800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:184442000-184448400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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