Variant report

Variant	rs5752839
Chromosome Location	chr22:29345890-29345891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29344969..29347183-chr22:29349320..29351089,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11912894	1.00[YRI][hapmap]
rs11913805	1.00[YRI][hapmap]
rs12627758	0.92[JPT][hapmap]
rs16986814	0.85[EUR][1000 genomes]
rs16986873	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2206061	1.00[MEX][hapmap]
rs2881637	0.85[EUR][1000 genomes]
rs4823000	0.92[JPT][hapmap]
rs5752830	0.80[EUR][1000 genomes]
rs5752842	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752851	0.92[JPT][hapmap]
rs5762890	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762891	0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762893	0.81[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762895	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762900	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762906	0.82[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762907	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762919	0.87[CEU][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap]
rs5997401	0.89[MEX][hapmap]
rs6005861	0.88[MEX][hapmap]
rs725281	0.92[JPT][hapmap]
rs7286026	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7288513	0.87[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7290364	0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73388860	0.85[EUR][1000 genomes]
rs73881200	0.90[AFR][1000 genomes]
rs73881201	0.90[AFR][1000 genomes]
rs8137589	0.95[EUR][1000 genomes]
rs8140640	0.92[JPT][hapmap]
rs9306461	0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs9625575	1.00[MEX][hapmap]
rs9625621	0.85[EUR][1000 genomes]
rs9625622	0.85[EUR][1000 genomes]
rs9625628	0.85[EUR][1000 genomes]
rs9625640	0.85[EUR][1000 genomes]
rs9625641	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9625645	0.88[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625647	0.85[ASN][1000 genomes]
rs9625657	1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs974369	0.84[ASN][1000 genomes]
rs974370	0.84[JPT][hapmap]

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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29332600-29347600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:29333800-29347800	Weak transcription	Gastric	stomach
3	chr22:29335800-29347800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:29336200-29347600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr22:29338600-29347600	Weak transcription	Left Ventricle	heart
6	chr22:29339600-29346800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr22:29339600-29347600	Weak transcription	Pancreas	Pancrea
8	chr22:29339800-29347600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr22:29339800-29352600	Weak transcription	Stomach Mucosa	stomach
10	chr22:29340000-29349200	Weak transcription	Aorta	Aorta
11	chr22:29343000-29346000	Enhancers	HepG2	liver
12	chr22:29343000-29346200	Weak transcription	Small Intestine	intestine
13	chr22:29343000-29347800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr22:29343400-29346200	Weak transcription	Brain Substantia Nigra	brain
15	chr22:29343600-29346000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr22:29343600-29346000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr22:29343600-29346400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr22:29343600-29346600	Weak transcription	Brain Angular Gyrus	brain
19	chr22:29343800-29346400	Weak transcription	Fetal Brain Male	brain
20	chr22:29343800-29347600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr22:29344000-29347000	Enhancers	Fetal Intestine Small	intestine
22	chr22:29344200-29347000	Enhancers	Fetal Intestine Large	intestine
23	chr22:29344400-29346000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr22:29344400-29346000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr22:29344400-29346600	Enhancers	Placenta	Placenta
26	chr22:29344400-29347400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr22:29344600-29347400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:29345000-29346000	Weak transcription	Liver	Liver
29	chr22:29345200-29347600	Weak transcription	Esophagus	oesophagus
30	chr22:29345200-29350800	Enhancers	Fetal Muscle Leg	muscle
31	chr22:29345400-29346400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr22:29345400-29346400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr22:29345400-29346400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr22:29345400-29347000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr22:29345400-29347000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr22:29345400-29349800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr22:29345400-29350000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr22:29345400-29350000	Enhancers	Fetal Lung	lung
39	chr22:29345600-29346000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr22:29345600-29346000	Weak transcription	Lung	lung
41	chr22:29345600-29346200	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr22:29345600-29346200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr22:29345600-29346400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr22:29345600-29346400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr22:29345600-29346600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr22:29345600-29346600	Enhancers	A549	lung
47	chr22:29345600-29346800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr22:29345600-29347000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr22:29345600-29347000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr22:29345600-29347600	Enhancers	Colon Smooth Muscle	Colon

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