Variant report

Variant	rs1541680
Chromosome Location	chr5:53304725-53304726
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	chr5:53304361..53306407-chr5:53311707..53313280,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10805455	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940353	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940354	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10940357	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11740817	0.97[ASN][1000 genomes]
rs11741082	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11742688	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11746045	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11746856	0.98[ASN][1000 genomes]
rs11747281	0.98[ASN][1000 genomes]
rs11747901	0.86[AMR][1000 genomes]
rs11747911	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12186486	0.94[ASN][1000 genomes]
rs12186509	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12189535	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521454	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12654393	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12659966	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1445887	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1541681	0.89[CEU][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541682	1.00[ASN][1000 genomes]
rs1542167	0.99[ASN][1000 genomes]
rs16881958	0.97[ASN][1000 genomes]
rs16881969	0.99[ASN][1000 genomes]
rs16881971	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2448	0.89[CEU][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs255746	0.88[ASN][1000 genomes]
rs255752	0.88[ASN][1000 genomes]
rs255755	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs255756	0.96[ASN][1000 genomes]
rs255757	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs255761	0.87[ASN][1000 genomes]
rs35027270	0.98[ASN][1000 genomes]
rs3776702	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776703	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776705	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776706	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776707	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776712	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776715	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776716	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776717	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776719	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3776720	0.89[CEU][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776721	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776722	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776723	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776724	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3776725	0.98[ASN][1000 genomes]
rs3776726	0.98[ASN][1000 genomes]
rs3822497	0.99[ASN][1000 genomes]
rs3822499	0.98[ASN][1000 genomes]
rs4311394	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4334835	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4334836	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4351101	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4588541	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5013866	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5024170	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56060165	0.92[ASN][1000 genomes]
rs56193151	0.93[ASN][1000 genomes]
rs56220547	0.94[ASN][1000 genomes]
rs57322591	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57898694	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58369491	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59061738	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60492935	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60652351	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6450175	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6450176	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66872223	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67199213	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67430852	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67473746	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67656636	0.97[ASN][1000 genomes]
rs67721004	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6866586	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6876198	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884760	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6884936	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6886510	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889847	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6898870	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7701922	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7707547	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7718193	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7732139	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7735253	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7736354	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9687611	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv830299	chr5:53207020-53386600	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53256800-53310000	Weak transcription	Primary T cells from cord blood	blood
2	chr5:53290600-53309600	Weak transcription	K562	blood
3	chr5:53295000-53305400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:53299000-53307000	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:53299200-53318000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:53302000-53306400	Enhancers	Liver	Liver
7	chr5:53303000-53306400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr5:53303000-53307000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr5:53303200-53307400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr5:53303400-53304800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:53303400-53304800	Enhancers	NHEK	skin
12	chr5:53303400-53305200	Enhancers	NHLF	lung
13	chr5:53303400-53307000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr5:53303400-53307000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:53303400-53307200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr5:53303600-53304800	Enhancers	Colon Smooth Muscle	Colon
17	chr5:53303600-53304800	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr5:53303600-53305000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:53303600-53305000	Enhancers	Fetal Intestine Large	intestine
20	chr5:53303600-53305000	Enhancers	Fetal Stomach	stomach
21	chr5:53303600-53305400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:53303600-53305800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr5:53303600-53305800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:53303600-53305800	Enhancers	H9 Cell Line	embryonic stem cell
25	chr5:53303600-53305800	Enhancers	Fetal Lung	lung
26	chr5:53303600-53306000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:53303600-53306000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:53303600-53306200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:53303600-53306400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:53303600-53306600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr5:53303600-53307200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:53303800-53306200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:53304000-53305000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr5:53304000-53305200	Flanking Active TSS	HepG2	liver
35	chr5:53304200-53305600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:53304400-53305800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:53304400-53306000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:53304400-53309000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:53304400-53309200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:53304400-53309200	Weak transcription	NHDF-Ad	bronchial
41	chr5:53304400-53310200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:53304600-53304800	Flanking Active TSS	A549	lung
43	chr5:53304600-53305600	Weak transcription	Ovary	ovary
44	chr5:53304600-53309000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:53304600-53309000	Weak transcription	HMEC	breast

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