Variant report

Variant	rs1459744
Chromosome Location	chr4:151157195-151157196
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	chr4:151151694..151154346-chr4:151156104..151158650,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10019650	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10031796	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12507489	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13107340	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1459745	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459746	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459747	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459748	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459749	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459751	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1459752	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1563790	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2169086	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2359927	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4025876	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4532220	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6535718	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6535719	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6535720	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6843630	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7658837	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7659254	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7667318	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7699202	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7699907	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9307870	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9307871	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9762327	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9997299	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9997489	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9999983	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151138800-151169800	Weak transcription	Spleen	Spleen
2	chr4:151139600-151177400	Weak transcription	Brain Substantia Nigra	brain
3	chr4:151139600-151181000	Weak transcription	Brain Angular Gyrus	brain
4	chr4:151140000-151175000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:151142200-151172200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:151146200-151169200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:151146400-151157400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:151146400-151157400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:151146400-151165600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:151146600-151165600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:151150800-151157800	Weak transcription	Fetal Kidney	kidney
12	chr4:151150800-151170800	Weak transcription	Pancreas	Pancrea
13	chr4:151151400-151157200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:151151400-151158400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:151151800-151165600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:151152000-151157200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:151152000-151160200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:151152400-151176400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:151152800-151164200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:151153600-151164800	Weak transcription	Right Atrium	heart
21	chr4:151153800-151158400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr4:151155000-151158000	Enhancers	NHDF-Ad	bronchial
23	chr4:151155000-151160400	Enhancers	NHLF	lung
24	chr4:151155200-151157400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:151155200-151157800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:151155200-151160600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:151155200-151161600	Genic enhancers	HSMM	muscle
28	chr4:151155600-151157400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
29	chr4:151156000-151157400	Enhancers	Fetal Brain Male	brain
30	chr4:151156000-151159200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:151156200-151159200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:151156200-151160800	Weak transcription	Brain Anterior Caudate	brain
33	chr4:151156200-151173000	Weak transcription	Fetal Intestine Small	intestine
34	chr4:151156400-151157400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:151156400-151158600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:151156400-151159000	Enhancers	Rectal Smooth Muscle	rectum
37	chr4:151156400-151163600	Weak transcription	Aorta	Aorta
38	chr4:151156400-151165200	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:151156400-151165600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:151156400-151169000	Weak transcription	Adipose Nuclei	Adipose
41	chr4:151156400-151169400	Weak transcription	Fetal Muscle Leg	muscle
42	chr4:151156400-151170600	Weak transcription	Right Ventricle	heart
43	chr4:151156400-151174200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:151156600-151157200	Enhancers	Hela-S3	cervix
45	chr4:151156600-151157800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:151156600-151158600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:151156600-151158800	Enhancers	Colon Smooth Muscle	Colon
48	chr4:151156600-151159200	Enhancers	Fetal Lung	lung
49	chr4:151156800-151157200	Genic enhancers	HSMMtube	muscle
50	chr4:151156800-151157600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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