Variant report

Variant	rs1204060
Chromosome Location	chr7:104963064-104963065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:104887620..104890465-chr7:104961186..104963915,2	MCF-7	breast:
2	chr7:104653252..104654991-chr7:104961759..104964369,2	MCF-7	breast:
3	chr7:104960628..104963813-chr7:104964024..104966847,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239569	Chromatin interaction
ENSG00000005483	Chromatin interaction
ENSG00000228393	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10227302	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10241415	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249170	0.80[ASN][1000 genomes]
rs10277120	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10281422	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10281886	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10953470	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10953474	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1121194	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761429	0.87[ASN][1000 genomes]
rs11765899	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1204056	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1204058	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204066	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204077	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1204078	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204080	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12334245	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12666949	0.80[ASN][1000 genomes]
rs12668097	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12671047	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705304	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12705306	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12705308	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226540	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13238191	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13239067	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17721991	0.80[ASN][1000 genomes]
rs2030776	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040913	0.80[ASN][1000 genomes]
rs2040914	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057883	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2057884	0.89[EUR][1000 genomes]
rs2237613	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2240463	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2299308	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299319	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34387062	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35601145	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35757884	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35851667	0.89[ASN][1000 genomes]
rs3779210	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3801278	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3801281	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3801282	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3801285	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3801999	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41562	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41563	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4496901	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4727621	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730072	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4730073	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4730080	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730081	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730082	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62484712	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466053	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6466055	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466056	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466057	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466064	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66599006	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6943183	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6952386	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6962856	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7357199	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7789569	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7800928	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801804	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7806591	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811681	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs917114	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9640686	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9649275	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34588	chr7:104737612-105153242	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised 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	17 gene(s)	inside rSNPs	diseases
2	esv2757233	chr7:104758250-105208492	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv2759549	chr7:104758250-105208492	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv8196	chr7:104763559-105155978	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv34580	chr7:104763580-105153242	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2758127	chr7:104766707-105110581	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1028228	chr7:104807207-105182998	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv932138	chr7:104826194-105152816	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1015688	chr7:104849770-105182998	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv1029832	chr7:104905057-105112489	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	esv2753646	chr7:104905588-104972800	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1023767	chr7:104931143-105190662	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv539049	chr7:104931143-105190662	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv1034689	chr7:104950564-105085879	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104939600-104966200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:104945400-104972600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:104948600-104988000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:104950600-104965600	Weak transcription	Primary B cells from cord blood	blood
5	chr7:104950600-104972200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:104950800-104963600	Weak transcription	Primary T cells from cord blood	blood
7	chr7:104950800-104965400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr7:104950800-104967800	Weak transcription	Gastric	stomach
9	chr7:104952200-104966200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:104954800-104971200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:104954800-104972400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:104956600-104963200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr7:104957400-104986800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:104957600-104966600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:104958000-104964000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:104958000-104968000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:104958000-104972000	Weak transcription	A549	lung
18	chr7:104958000-104983200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr7:104958800-104973000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:104960000-104969200	Weak transcription	Thymus	Thymus
21	chr7:104960400-104963600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr7:104960400-104963800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr7:104960800-104968400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr7:104961400-104963800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:104961400-104963800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:104961400-104969400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:104961400-104972200	Weak transcription	Right Ventricle	heart
28	chr7:104961600-104972200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:104961600-104972200	Weak transcription	Lung	lung
30	chr7:104961600-104973000	Weak transcription	Ovary	ovary
31	chr7:104961600-104980200	Weak transcription	Psoas Muscle	Psoas
32	chr7:104961800-104973000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:104962400-104963400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr7:104962400-104966800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr7:104962600-104963400	Enhancers	Left Ventricle	heart
36	chr7:104962600-104963800	Weak transcription	Dnd41	blood
37	chr7:104962600-104965400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr7:104962800-104963200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr7:104962800-104963200	Enhancers	Fetal Stomach	stomach
40	chr7:104962800-104963600	Enhancers	Brain Anterior Caudate	brain
41	chr7:104962800-104963600	Enhancers	Fetal Muscle Leg	muscle
42	chr7:104962800-104964000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr7:104962800-104966000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:104962800-104992600	Weak transcription	Fetal Intestine Small	intestine
45	chr7:104963000-104963400	Weak transcription	Pancreas	Pancrea
46	chr7:104963000-104963400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr7:104963000-104964200	Enhancers	Brain Hippocampus Middle	brain
48	chr7:104963000-104966200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr7:104963000-104983000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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