Variant report

Variant	rs2493420
Chromosome Location	chr1:120484421-120484422
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	chr1:120478050..120480567-chr1:120483456..120486194,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134250	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10127888	0.94[ASW][hapmap];0.83[CEU][hapmap]
rs10494235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923926	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923929	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923931	0.94[ASW][hapmap];0.83[CEU][hapmap]
rs1493694	0.83[CEU][hapmap]
rs1493695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[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];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1493698	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027447	0.94[ASW][hapmap]
rs2453040	0.83[CEU][hapmap]
rs2453042	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453055	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453058	0.94[ASW][hapmap];0.83[CEU][hapmap]
rs2487568	0.91[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493389	0.81[CEU][hapmap]
rs2493391	0.83[CEU][hapmap]
rs2493392	0.94[ASW][hapmap];0.83[CEU][hapmap]
rs2493394	0.83[CEU][hapmap]
rs2493398	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs2493416	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2493419	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641317	0.94[ASW][hapmap];0.83[CEU][hapmap]
rs2641338	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641352	0.94[ASW][hapmap]
rs2793823	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793827	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793829	0.94[ASW][hapmap];0.83[CEU][hapmap]
rs2793830	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793831	0.94[ASW][hapmap];0.83[CEU][hapmap]
rs2934381	0.94[ASW][hapmap];0.83[CEU][hapmap]
rs2934387	0.94[ASW][hapmap];0.83[CEU][hapmap]
rs327194	0.80[CEU][hapmap]
rs327196	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3897478	0.94[ASW][hapmap]
rs4659250	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]
rs5025718	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs699780	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515431	0.83[CEU][hapmap]
rs7534585	0.83[CEU][hapmap]
rs7534586	0.94[ASW][hapmap];0.83[CEU][hapmap]
rs835573	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835574	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835575	0.94[ASW][hapmap]
rs835576	0.82[ASW][hapmap]
rs947273	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];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	chr1:120452000-120485600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:120455800-120486800	Strong transcription	Liver	Liver
3	chr1:120456200-120488000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:120468400-120495800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:120468400-120506200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:120468400-120507400	Weak transcription	Right Ventricle	heart
7	chr1:120468600-120496000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:120468600-120532800	Weak transcription	Stomach Mucosa	stomach
9	chr1:120469600-120485600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:120474800-120484600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:120475200-120484800	Strong transcription	NHDF-Ad	bronchial
12	chr1:120475200-120484800	Strong transcription	Osteobl	bone
13	chr1:120475400-120484800	Strong transcription	HSMM	muscle
14	chr1:120475600-120484800	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:120475600-120485600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:120475800-120484600	Strong transcription	HSMMtube	muscle
17	chr1:120475800-120484800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:120476000-120484600	Strong transcription	HMEC	breast
19	chr1:120476000-120484800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:120476400-120484600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr1:120476400-120507400	Weak transcription	Brain Angular Gyrus	brain
22	chr1:120476600-120484600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:120476800-120484600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:120476800-120484800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:120476800-120485000	Strong transcription	Dnd41	blood
26	chr1:120476800-120485600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:120476800-120486000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:120476800-120488800	Strong transcription	Primary B cells from cord blood	blood
29	chr1:120477000-120486600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:120477000-120497200	Weak transcription	Small Intestine	intestine
31	chr1:120477400-120484600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:120477400-120488000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:120477600-120484600	Strong transcription	Fetal Kidney	kidney
34	chr1:120478200-120484800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:120478800-120508800	Weak transcription	A549	lung
36	chr1:120478800-120511000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:120479000-120511000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr1:120479200-120490800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:120479200-120491000	Weak transcription	Fetal Brain Male	brain
40	chr1:120479600-120493000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:120479600-120504000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:120480400-120507800	Weak transcription	Fetal Brain Female	brain
43	chr1:120480600-120490000	Weak transcription	Brain Germinal Matrix	brain
44	chr1:120480600-120490800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:120480600-120490800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:120480600-120490800	Weak transcription	HepG2	liver
47	chr1:120480600-120491000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:120480600-120492400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:120480600-120492600	Weak transcription	HUVEC	blood vessel
50	chr1:120480600-120495000	Weak transcription	H1 Cell Line	embryonic stem cell

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