Variant report

Variant	rs2044238
Chromosome Location	chr5:112479902-112479903
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	chr5:112476798..112478381-chr5:112478430..112480202,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10463646	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519334	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs13168126	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13183116	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13190040	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1562016	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2044239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165930	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs2416303	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2416305	0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2416306	0.87[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35334140	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3922563	0.83[CHB][hapmap]
rs3922583	0.84[CHB][hapmap]
rs4634343	0.84[EUR][1000 genomes]
rs4705782	0.80[CEU][hapmap]
rs4705783	0.83[CHB][hapmap]
rs4705789	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4705794	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705795	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4705796	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705797	0.81[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs7707546	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7720549	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7720866	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7726679	0.81[CEU][hapmap];0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs935159	0.87[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv599400	chr5:112477948-112479902	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv1850895	chr5:112479748-112481426	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112467400-112493200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:112470200-112491000	Weak transcription	Fetal Kidney	kidney
3	chr5:112470600-112482000	Weak transcription	Fetal Heart	heart
4	chr5:112474800-112482400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:112477000-112483200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:112477200-112483200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr5:112477200-112485400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:112477400-112481400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:112477400-112482000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:112477400-112482400	Weak transcription	Adipose Nuclei	Adipose
11	chr5:112477400-112482600	Weak transcription	NHLF	lung
12	chr5:112477400-112486600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:112477400-112486600	Weak transcription	Right Atrium	heart
14	chr5:112477400-112489200	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:112477400-112500600	Weak transcription	Fetal Stomach	stomach
16	chr5:112477600-112481200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:112477600-112482600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:112477600-112482800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:112477600-112482800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:112477600-112483000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:112477800-112482400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:112478000-112482400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:112478000-112483000	Weak transcription	Left Ventricle	heart
24	chr5:112478000-112485600	Weak transcription	Pancreas	Pancrea
25	chr5:112478000-112497000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:112478200-112480600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:112478200-112480800	Weak transcription	Esophagus	oesophagus
28	chr5:112478200-112482400	Weak transcription	HSMMtube	muscle
29	chr5:112478400-112480800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:112478400-112482400	Weak transcription	NHDF-Ad	bronchial
31	chr5:112478400-112483000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:112478600-112480800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:112478600-112481600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:112478600-112481600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:112478600-112481600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:112478600-112481800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:112478600-112482000	Weak transcription	Osteobl	bone
38	chr5:112478600-112483000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:112478800-112480200	Weak transcription	Ovary	ovary
40	chr5:112478800-112480600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:112478800-112480600	Weak transcription	HMEC	breast
42	chr5:112478800-112480600	Weak transcription	NHEK	skin
43	chr5:112478800-112482000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr5:112478800-112483000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:112479200-112485200	Weak transcription	Liver	Liver
46	chr5:112479200-112490000	Weak transcription	Aorta	Aorta
47	chr5:112479400-112489600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:112479600-112481000	Weak transcription	Primary T cells from cord blood	blood
49	chr5:112479600-112482000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:112479800-112480400	Enhancers	Right Ventricle	heart

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