Variant report

Variant	rs2453040
Chromosome Location	chr1:120529750-120529751
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:120519289..120523601-chr1:120528205..120531823,5	MCF-7	breast:
2	chr1:120529008..120531622-chr1:120534820..120537508,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10127888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494235	0.81[CEU][hapmap]
rs10923926	0.84[CEU][hapmap]
rs10923931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493691	0.88[AFR][1000 genomes]
rs1493694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493695	0.84[CEU][hapmap]
rs1493696	0.84[CEU][hapmap]
rs17024432	1.00[CHB][hapmap]
rs17186372	1.00[JPT][hapmap]
rs17258599	1.00[JPT][hapmap]
rs1738647	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027447	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453044	0.83[CEU][hapmap]
rs2453056	0.83[CEU][hapmap]
rs2453058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493390	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493410	0.83[CEU][hapmap]
rs2493411	0.83[CEU][hapmap]
rs2493413	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493415	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2493420	0.83[CEU][hapmap]
rs2641316	0.83[CEU][hapmap]
rs2641317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641346	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2641348	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641352	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793830	0.83[CEU][hapmap]
rs2793831	1.00[CEU][hapmap];1.00[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]
rs2843024	1.00[JPT][hapmap]
rs2934381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327194	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs327196	0.84[CEU][hapmap]
rs327205	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs327206	0.91[CEU][hapmap]
rs3897478	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911328	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs406767	0.82[ASN][1000 genomes]
rs4659250	0.84[CEU][hapmap]
rs5025718	0.83[CEU][hapmap]
rs56302051	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6685892	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688004	0.83[CEU][hapmap]
rs699779	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72697237	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835574	0.83[CEU][hapmap]
rs835575	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835576	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9662844	1.00[JPT][hapmap]

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:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120468600-120532800	Weak transcription	Stomach Mucosa	stomach
2	chr1:120491200-120538800	Weak transcription	Fetal Brain Male	brain
3	chr1:120508600-120529800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:120509000-120533000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:120509800-120557600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:120510200-120532800	Weak transcription	Brain Anterior Caudate	brain
7	chr1:120510200-120538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:120510200-120552200	Weak transcription	HUVEC	blood vessel
9	chr1:120510400-120529800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:120510800-120532800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:120510800-120533000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:120510800-120557400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:120511600-120557800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:120512400-120543600	Weak transcription	Fetal Intestine Small	intestine
15	chr1:120512600-120532800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:120514400-120543400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:120514400-120549400	Weak transcription	Gastric	stomach
18	chr1:120514600-120530600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:120515000-120532800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:120518800-120533000	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:120521200-120549400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:120523800-120546800	Weak transcription	Esophagus	oesophagus
23	chr1:120524400-120543600	Weak transcription	Spleen	Spleen
24	chr1:120525600-120530200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:120525600-120530800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:120525600-120532800	Weak transcription	Fetal Stomach	stomach
27	chr1:120525600-120557800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:120526200-120532800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:120526400-120529800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:120527000-120529800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:120527200-120529800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:120527200-120529800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr1:120527200-120529800	Genic enhancers	Osteobl	bone
34	chr1:120527200-120530000	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr1:120527400-120529800	Strong transcription	Liver	Liver
36	chr1:120527400-120529800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr1:120527400-120529800	Genic enhancers	NHDF-Ad	bronchial
38	chr1:120527400-120530000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:120527600-120533000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:120527600-120550000	Weak transcription	Lung	lung
41	chr1:120527800-120530200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:120527800-120532800	Weak transcription	Ovary	ovary
43	chr1:120527800-120542400	Weak transcription	Brain Germinal Matrix	brain
44	chr1:120527800-120558200	Weak transcription	Brain Angular Gyrus	brain
45	chr1:120528000-120532800	Weak transcription	Fetal Kidney	kidney
46	chr1:120528600-120530000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:120528600-120530000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:120528800-120529800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:120528800-120530000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:120529000-120529800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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