Variant report

Variant	rs601225
Chromosome Location	chr3:101580650-101580651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101580592..101582802-chr3:101828628..101830530,2	MCF-7	breast:
2	chr3:101580218..101581720-chr3:101588076..101590866,2	MCF-7	breast:
3	chr3:101578560..101581367-chr3:101581582..101584518,2	K562	blood:
4	chr3:101579733..101582231-chr3:101586214..101587779,2	K562	blood:
5	chr3:101580233..101583305-chr3:101583539..101587292,4	MCF-7	breast:
6	chr3:101580490..101582879-chr3:101701319..101703649,2	MCF-7	breast:
7	chr3:101580255..101583054-chr3:101925277..101927945,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs14134	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2925332	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2925333	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2926538	0.80[ASN][1000 genomes]
rs2926539	0.83[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2926540	0.83[CEU][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2929922	0.80[ASN][1000 genomes]
rs587555	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs592332	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs592779	0.83[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs599849	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs617688	0.81[CHD][hapmap]
rs618901	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs622122	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs641432	0.80[ASN][1000 genomes]
rs654219	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs665374	0.83[CEU][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs677011	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs678354	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs680508	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs681573	0.83[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs688058	0.82[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs694293	0.83[CEU][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs694936	0.81[CHD][hapmap];0.80[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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101570400-101598400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:101570800-101580800	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:101570800-101580800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:101571000-101581400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:101571200-101581000	Strong transcription	Colon Smooth Muscle	Colon
6	chr3:101571200-101582000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:101571400-101580800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:101571400-101581400	Strong transcription	NHLF	lung
9	chr3:101572200-101581400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:101572600-101581000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:101572600-101581200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:101572600-101581400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:101572600-101581800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:101572600-101583400	Strong transcription	Primary hematopoietic stem cells	blood
15	chr3:101572800-101580800	Strong transcription	HMEC	breast
16	chr3:101574400-101580800	Strong transcription	A549	lung
17	chr3:101574400-101582400	Weak transcription	Fetal Heart	heart
18	chr3:101575800-101581400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:101576200-101581000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:101576400-101580800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:101576400-101580800	Strong transcription	Placenta	Placenta
22	chr3:101576400-101580800	Strong transcription	NHDF-Ad	bronchial
23	chr3:101576400-101581200	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr3:101576400-101581200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:101576400-101581400	Strong transcription	Primary T cells from cord blood	blood
26	chr3:101576400-101581400	Strong transcription	Stomach Smooth Muscle	stomach
27	chr3:101576400-101581400	Strong transcription	HSMMtube	muscle
28	chr3:101576400-101581600	Strong transcription	Adipose Nuclei	Adipose
29	chr3:101576400-101581600	Strong transcription	Liver	Liver
30	chr3:101576400-101582000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:101576400-101582000	Strong transcription	Left Ventricle	heart
32	chr3:101576400-101582200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:101576400-101586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:101576400-101586800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:101576600-101581000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:101576600-101581000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr3:101576600-101581200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:101576600-101581400	Strong transcription	NH-A	brain
39	chr3:101576600-101581800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:101576600-101582000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr3:101576600-101586200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:101577200-101586200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:101577400-101580800	Strong transcription	Brain Anterior Caudate	brain
44	chr3:101577400-101582000	Strong transcription	HSMM	muscle
45	chr3:101577400-101582000	Strong transcription	Osteobl	bone
46	chr3:101577600-101580800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:101577600-101581000	Weak transcription	Psoas Muscle	Psoas
48	chr3:101577600-101581200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:101577600-101581400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr3:101577600-101581400	Strong transcription	Duodenum Mucosa	Duodenum

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