Variant report

Variant	rs3901010
Chromosome Location	chr5:106765839-106765840
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:106763769..106766443-chr5:107007401..107010371,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11242636	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11956440	0.88[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs13178242	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs13182976	0.88[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs1835111	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs34366978	0.81[EUR][1000 genomes]
rs34583348	0.82[ASN][1000 genomes]
rs35021422	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3756544	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs3776792	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3797510	0.88[CEU][hapmap]
rs3797513	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs3797516	0.94[CEU][hapmap];0.91[CHB][hapmap]
rs3797517	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs3797521	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs3797527	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3873122	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs3873123	0.83[EUR][1000 genomes]
rs3909931	0.85[EUR][1000 genomes]
rs58696640	0.80[EUR][1000 genomes]
rs66505151	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6868410	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs7703776	0.88[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap]

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	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106751800-106767800	Weak transcription	Stomach Mucosa	stomach
2	chr5:106754000-106767600	Weak transcription	Fetal Stomach	stomach
3	chr5:106756400-106768200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:106756600-106772000	Weak transcription	Esophagus	oesophagus
5	chr5:106758600-106767800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:106758600-106767800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:106758600-106767800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:106758600-106767800	Weak transcription	Left Ventricle	heart
9	chr5:106758600-106771200	Weak transcription	Right Ventricle	heart
10	chr5:106758600-106772000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:106758600-106785000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:106759600-106767600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:106761600-106766200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:106761800-106767200	Weak transcription	Adipose Nuclei	Adipose
15	chr5:106761800-106767600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:106762200-106767200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:106762200-106767600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:106762200-106767600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:106762200-106767600	Weak transcription	HSMMtube	muscle
20	chr5:106762200-106767600	Weak transcription	NH-A	brain
21	chr5:106762200-106771600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr5:106762200-106772200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:106762600-106767400	Weak transcription	NHEK	skin
24	chr5:106762600-106767600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:106762800-106767400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:106763000-106767400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:106763000-106772000	Weak transcription	Right Atrium	heart
28	chr5:106763200-106767200	Weak transcription	Hela-S3	cervix
29	chr5:106763200-106767600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:106763200-106767800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr5:106763200-106773600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:106763200-106773600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:106763400-106771800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:106763800-106767000	Enhancers	Fetal Heart	heart
35	chr5:106764400-106766200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:106764400-106767200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:106764600-106766000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:106765400-106766200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:106765400-106766200	Enhancers	Fetal Lung	lung
40	chr5:106765400-106767000	Weak transcription	GM12878-XiMat	blood
41	chr5:106765600-106766000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:106765600-106766400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr5:106765600-106766400	Enhancers	HSMM	muscle
44	chr5:106765600-106767400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:106765800-106766000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:106765800-106766000	Flanking Active TSS	NHLF	lung
47	chr5:106765800-106766000	Enhancers	Osteobl	bone
48	chr5:106765800-106766200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:106765800-106766200	Enhancers	Brain Germinal Matrix	brain
50	chr5:106765800-106766200	Enhancers	HMEC	breast

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