Variant report

Variant	rs1339572
Chromosome Location	chr1:184565572-184565573
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184564795..184566904-chr1:184571441..184573891,2	MCF-7	breast:
2	chr1:184557585..184559770-chr1:184565063..184567292,3	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1006224	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10465489	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12072648	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12747629	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1339571	0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs61825243	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking 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	69 gene(s)	inside rSNPs	diseases
4	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS 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	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1339572	RALGPS2	cis	cerebellum	SCAN
rs1339572	C1orf125	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184546200-184566600	Weak transcription	Left Ventricle	heart
2	chr1:184547800-184580000	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:184553200-184566200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:184553200-184566600	Weak transcription	Fetal Stomach	stomach
5	chr1:184553600-184566200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:184553600-184566200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:184557000-184566400	Weak transcription	Psoas Muscle	Psoas
8	chr1:184557000-184566400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:184557200-184566400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:184557200-184574000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:184557200-184591600	Weak transcription	Aorta	Aorta
12	chr1:184558600-184566400	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:184558600-184568000	Weak transcription	Pancreas	Pancrea
14	chr1:184558600-184572600	Weak transcription	Lung	lung
15	chr1:184558800-184566600	Weak transcription	Fetal Lung	lung
16	chr1:184559000-184588400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:184559200-184566600	Weak transcription	Right Ventricle	heart
18	chr1:184559200-184580400	Weak transcription	Adipose Nuclei	Adipose
19	chr1:184559400-184580400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:184559600-184578000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:184559800-184566200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:184559800-184566400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:184560200-184566600	Weak transcription	Liver	Liver
24	chr1:184560400-184565600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:184560400-184566400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:184560400-184566400	Weak transcription	Small Intestine	intestine
27	chr1:184560600-184571400	Weak transcription	Fetal Intestine Large	intestine
28	chr1:184560600-184591000	Weak transcription	Fetal Intestine Small	intestine
29	chr1:184562400-184566400	Weak transcription	Placenta	Placenta
30	chr1:184562400-184580000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:184562600-184566000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:184562600-184566600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:184562800-184565600	Enhancers	A549	lung
34	chr1:184562800-184566200	Weak transcription	Stomach Mucosa	stomach
35	chr1:184562800-184579600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:184563000-184573200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:184563200-184566800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:184563400-184566600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:184563600-184565600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:184563800-184573600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:184564200-184580200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:184564200-184580200	Weak transcription	Ovary	ovary
43	chr1:184564400-184565600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:184564400-184574200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:184564400-184578200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:184564600-184565600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:184564600-184565600	Enhancers	Osteobl	bone
48	chr1:184564600-184565800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:184564600-184565800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:184564600-184566200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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