Variant report

Variant	rs4597553
Chromosome Location	chr2:73006888-73006889
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73005561..73008287-chr2:73013909..73016278,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10204141	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10496187	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11126378	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs11126382	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11126386	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11689339	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs11693376	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11884266	0.86[YRI][hapmap]
rs11886503	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11892598	0.89[YRI][hapmap]
rs12614041	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12615163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12615875	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12619068	1.00[CEU][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12619565	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13008515	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1532970	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1562361	0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs17008315	0.93[YRI][hapmap]
rs17008360	0.81[CEU][hapmap]
rs17008369	0.81[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs17008371	0.89[YRI][hapmap];0.94[AFR][1000 genomes]
rs1876488	1.00[CEU][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1876489	1.00[JPT][hapmap]
rs1876490	1.00[JPT][hapmap]
rs2063168	0.89[EUR][1000 genomes]
rs2068410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[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]
rs35666345	0.89[ASN][1000 genomes]
rs4852896	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4852897	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4852900	0.87[EUR][1000 genomes]
rs55642420	0.86[AFR][1000 genomes]
rs55749009	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55802296	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56058174	0.93[AFR][1000 genomes]
rs56181835	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56711961	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57264301	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58890506	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59216875	0.93[AFR][1000 genomes]
rs59615613	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60284189	0.95[AFR][1000 genomes]
rs60314340	0.84[AFR][1000 genomes]
rs60584321	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61619102	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61736520	0.91[AFR][1000 genomes]
rs66469454	0.84[AFR][1000 genomes]
rs66509842	0.98[AFR][1000 genomes]
rs66794803	0.90[AFR][1000 genomes]
rs6713143	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs6713712	0.90[YRI][hapmap]
rs6716335	1.00[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6736649	0.85[AFR][1000 genomes]
rs6761253	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67919884	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67927720	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7567893	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7577528	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7586339	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586886	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7593084	0.93[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7600718	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7604402	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7607226	1.00[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs970577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72923000-73008600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:72985200-73008400	Weak transcription	Right Atrium	heart
3	chr2:72985200-73015800	Weak transcription	Ovary	ovary
4	chr2:72989400-73015800	Weak transcription	Placenta	Placenta
5	chr2:72990800-73018400	Weak transcription	Aorta	Aorta
6	chr2:72991200-73015800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:72991200-73015800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:72991200-73023000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:72992400-73007600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:72993600-73009000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:72999800-73022000	Weak transcription	Right Ventricle	heart
12	chr2:73002600-73007600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:73002600-73008000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:73002600-73011600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:73002600-73012800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:73005000-73007600	Enhancers	HUVEC	blood vessel
17	chr2:73005200-73008600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:73005400-73016200	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:73005800-73007200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:73005800-73007200	Weak transcription	Adipose Nuclei	Adipose
21	chr2:73005800-73007200	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr2:73005800-73007400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:73005800-73011000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:73005800-73011200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:73005800-73012600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:73005800-73015800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:73005800-73016200	Weak transcription	HSMM	muscle
28	chr2:73006000-73007400	Weak transcription	HepG2	liver
29	chr2:73006000-73007400	Weak transcription	NHEK	skin
30	chr2:73006000-73007600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:73006000-73007800	Weak transcription	Fetal Kidney	kidney
32	chr2:73006000-73009800	Weak transcription	Small Intestine	intestine
33	chr2:73006200-73007600	Weak transcription	HMEC	breast
34	chr2:73006400-73007600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:73006400-73007600	Enhancers	A549	lung
36	chr2:73006400-73011200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:73006600-73007200	Enhancers	Left Ventricle	heart
38	chr2:73006600-73008600	Enhancers	Brain Substantia Nigra	brain
39	chr2:73006600-73008800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr2:73006600-73008800	Enhancers	Fetal Lung	lung
41	chr2:73006600-73009000	Enhancers	Hela-S3	cervix
42	chr2:73006600-73009200	Enhancers	Brain Hippocampus Middle	brain
43	chr2:73006800-73007000	Enhancers	Brain Cingulate Gyrus	brain
44	chr2:73006800-73007000	Flanking Active TSS	Fetal Heart	heart
45	chr2:73006800-73007800	Weak transcription	Brain Angular Gyrus	brain
46	chr2:73006800-73008600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:73006800-73009000	Enhancers	Brain Anterior Caudate	brain

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