Variant report

Variant	rs4659250
Chromosome Location	chr1:120498086-120498087
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120445668..120448303-chr1:120496593..120499239,2	MCF-7	breast:
2	chr1:120497342..120499963-chr1:120501229..120503818,2	K562	blood:
3	chr1:120497371..120500644-chr1:120500886..120502756,3	MCF-7	breast:
4	chr1:120493088..120496075-chr1:120496488..120499271,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10127888	0.83[CEU][hapmap]
rs10494235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923926	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923931	0.83[CEU][hapmap]
rs1493694	0.83[CEU][hapmap]
rs1493695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1493698	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453040	0.84[CEU][hapmap]
rs2453042	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453055	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453058	0.83[CEU][hapmap]
rs2487568	0.91[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493389	0.83[CEU][hapmap]
rs2493391	0.84[CEU][hapmap]
rs2493392	0.83[CEU][hapmap]
rs2493394	0.84[CEU][hapmap]
rs2493398	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493416	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2493419	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641317	0.83[CEU][hapmap]
rs2641338	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793823	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793827	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793829	0.83[CEU][hapmap]
rs2793830	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793831	0.83[CEU][hapmap]
rs2934381	0.83[CEU][hapmap]
rs2934387	0.83[CEU][hapmap]
rs327194	0.82[CEU][hapmap]
rs327196	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs5025718	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs699780	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515431	0.83[CEU][hapmap]
rs7534585	0.84[CEU][hapmap]
rs7534586	0.83[CEU][hapmap]
rs835573	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835574	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947273	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1816057	chr1:120469050-120697156	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv1818054	chr1:120469050-120697156	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv1844863	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv1850218	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv427730	chr1:120469050-120697156	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120468400-120506200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:120468400-120507400	Weak transcription	Right Ventricle	heart
3	chr1:120468600-120532800	Weak transcription	Stomach Mucosa	stomach
4	chr1:120476400-120507400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:120478800-120508800	Weak transcription	A549	lung
6	chr1:120478800-120511000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:120479000-120511000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:120479600-120504000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:120480400-120507800	Weak transcription	Fetal Brain Female	brain
10	chr1:120480600-120503600	Weak transcription	Brain Substantia Nigra	brain
11	chr1:120480600-120507400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:120484400-120506000	Weak transcription	Gastric	stomach
13	chr1:120484600-120505800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:120488800-120510400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:120489200-120499000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:120490000-120499000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:120490000-120500000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:120490000-120512400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:120490000-120514400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:120490000-120517600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:120490200-120498200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:120490200-120512600	Strong transcription	Primary T cells from cord blood	blood
23	chr1:120490200-120512600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:120490200-120521000	Strong transcription	Primary B cells from cord blood	blood
25	chr1:120490400-120498200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:120490400-120500800	Strong transcription	Adipose Nuclei	Adipose
27	chr1:120490400-120502600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:120490400-120512600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:120490600-120498200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:120490800-120498200	Strong transcription	NHEK	skin
31	chr1:120490800-120498600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:120490800-120499800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:120490800-120501400	Strong transcription	Fetal Thymus	thymus
34	chr1:120490800-120502600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:120490800-120502800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:120490800-120515000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:120491000-120498200	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:120491000-120498200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:120491200-120498800	Strong transcription	HMEC	breast
40	chr1:120491200-120499800	Weak transcription	HepG2	liver
41	chr1:120491200-120510800	Weak transcription	Brain Germinal Matrix	brain
42	chr1:120491200-120538800	Weak transcription	Fetal Brain Male	brain
43	chr1:120491400-120500000	Strong transcription	NH-A	brain
44	chr1:120491600-120499000	Weak transcription	Fetal Heart	heart
45	chr1:120491800-120498200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:120491800-120498200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:120491800-120498400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:120491800-120498800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr1:120491800-120499600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:120491800-120499600	Strong transcription	Osteobl	bone

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