Variant report

Variant	rs1146480
Chromosome Location	chr1:95045362-95045363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:95044875..95047288-chr1:95048137..95050937,2	MCF-7	breast:
2	chr1:95043796..95046993-chr1:95048870..95051582,3	K562	blood:
3	chr1:95043796..95046691-chr1:95048870..95051582,2	K562	blood:
4	chr1:95006436..95008771-chr1:95043871..95046807,3	MCF-7	breast:
5	chr1:95044965..95045519-chr1:95065172..95065776,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117525	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1041041	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1041042	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11165158	0.82[ASN][1000 genomes]
rs1146473	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1146474	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1146476	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146477	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146482	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146484	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1146485	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1146487	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1146489	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1146491	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1146492	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1146494	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1146496	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1146498	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1146500	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1146501	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11485356	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12075529	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12354005	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1245215	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1303132	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1303134	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1303135	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1303137	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1303138	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1303139	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1324217	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1408341	0.85[ASN][1000 genomes]
rs1578535	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1612481	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1772904	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1772911	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1778205	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778206	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1778207	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1778208	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1778223	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1778226	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2093843	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2762509	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2794475	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2794476	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2794479	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2971946	0.85[ASN][1000 genomes]
rs2971947	0.88[ASN][1000 genomes]
rs2985287	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2996292	0.85[ASN][1000 genomes]
rs6668501	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs68169338	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs927633	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs927634	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs927635	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs927636	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs968661	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs968662	0.90[AMR][1000 genomes];0.94[EUR][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	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871279	chr1:95028981-95083836	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95038600-95046200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:95044200-95046600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:95044200-95047000	Enhancers	NHEK	skin
4	chr1:95044200-95048400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:95044400-95047000	Enhancers	NHLF	lung
6	chr1:95044400-95048200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr1:95044400-95048400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:95044400-95048400	Enhancers	HMEC	breast
9	chr1:95044600-95045600	Enhancers	NH-A	brain
10	chr1:95044600-95046000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:95044600-95046200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:95044600-95046200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:95044600-95046400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:95044600-95046400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:95044600-95046400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:95044600-95046400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:95044600-95046400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:95044600-95046400	Flanking Active TSS	Hela-S3	cervix
19	chr1:95044600-95046800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:95044600-95047000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:95044600-95047400	Enhancers	HSMMtube	muscle
22	chr1:95044800-95046400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:95044800-95046400	Enhancers	Placenta	Placenta
24	chr1:95044800-95046400	Enhancers	Osteobl	bone
25	chr1:95045000-95045600	Enhancers	K562	blood
26	chr1:95045000-95045800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr1:95045000-95046000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr1:95045000-95046000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:95045000-95046200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr1:95045000-95046200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:95045000-95046200	Enhancers	HSMM	muscle
32	chr1:95045000-95046400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:95045000-95046400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:95045000-95046400	Enhancers	Aorta	Aorta
35	chr1:95045000-95046400	Enhancers	NHDF-Ad	bronchial
36	chr1:95045200-95045600	Enhancers	H9 Cell Line	embryonic stem cell
37	chr1:95045200-95045600	Enhancers	Fetal Muscle Leg	muscle
38	chr1:95045200-95045600	Enhancers	A549	lung
39	chr1:95045200-95045800	Enhancers	H1 Cell Line	embryonic stem cell
40	chr1:95045200-95045800	Enhancers	Fetal Intestine Small	intestine
41	chr1:95045200-95045800	Enhancers	Ovary	ovary
42	chr1:95045200-95046000	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr1:95045200-95046000	Enhancers	Esophagus	oesophagus
44	chr1:95045200-95046000	Enhancers	Fetal Intestine Large	intestine
45	chr1:95045200-95046000	Enhancers	Right Atrium	heart
46	chr1:95045200-95046000	Enhancers	Stomach Mucosa	stomach
47	chr1:95045200-95046200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr1:95045200-95046200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr1:95045200-95046200	Enhancers	Lung	lung
50	chr1:95045200-95046400	Enhancers	HUES64 Cell Line	embryonic stem cell

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