Variant report

Variant	rs56219066
Chromosome Location	chr5:95242931-95242932
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	chr5:95242612..95244160-chr5:95296224..95298880,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251314	Chromatin interaction
ENSG00000118985	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10035477	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10069748	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10070197	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1043381	0.99[EUR][1000 genomes]
rs1057963	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1057964	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11135441	0.82[EUR][1000 genomes]
rs11135442	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11738768	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11739652	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11741563	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741590	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11744881	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13361341	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13361837	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1423268	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1423269	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1458017	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1458018	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1458019	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs147295	0.83[EUR][1000 genomes]
rs154460	0.81[EUR][1000 genomes]
rs17085231	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17085249	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17085266	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1841010	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2015159	0.91[EUR][1000 genomes]
rs2042340	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2270554	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2348984	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2546191	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2547997	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2548594	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2829	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777182	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777183	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777184	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777185	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777188	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777189	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777190	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777192	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777193	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777194	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777196	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777197	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777200	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777201	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777202	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777203	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777204	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777208	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3815768	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4563648	0.91[EUR][1000 genomes]
rs4642392	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56156268	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6556893	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6877329	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6879652	0.99[EUR][1000 genomes]
rs6885567	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6889029	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6890954	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7702674	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7716691	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs889302	0.91[EUR][1000 genomes]
rs9314162	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs967546	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9986236	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95213000-95244600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:95214400-95247800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:95214400-95251800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:95215800-95244600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:95218200-95246200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:95219800-95244400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:95220000-95245200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr5:95220600-95243200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:95221600-95252200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:95222000-95252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:95223000-95259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:95226400-95263600	Weak transcription	Colonic Mucosa	Colon
13	chr5:95227400-95251600	Weak transcription	Primary T cells from cord blood	blood
14	chr5:95227400-95253800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:95227600-95244600	Weak transcription	Small Intestine	intestine
16	chr5:95231200-95254000	Weak transcription	Fetal Stomach	stomach
17	chr5:95231800-95243200	Weak transcription	Lung	lung
18	chr5:95231800-95244200	Weak transcription	Ovary	ovary
19	chr5:95232200-95244600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:95232400-95255200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:95232600-95244600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:95232600-95247400	Weak transcription	Aorta	Aorta
23	chr5:95232800-95243000	Weak transcription	Esophagus	oesophagus
24	chr5:95232800-95244200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:95232800-95244600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:95234200-95251800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr5:95234400-95244800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:95234400-95251800	Weak transcription	Fetal Thymus	thymus
29	chr5:95234600-95244600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:95235000-95251800	Weak transcription	Primary B cells from cord blood	blood
31	chr5:95236000-95247600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:95236000-95251600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr5:95236200-95254200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:95236400-95243000	Weak transcription	Psoas Muscle	Psoas
35	chr5:95236400-95243200	Weak transcription	Adipose Nuclei	Adipose
36	chr5:95236400-95249600	Weak transcription	Fetal Lung	lung
37	chr5:95236400-95276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:95236600-95243200	Weak transcription	Fetal Heart	heart
39	chr5:95236600-95244600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:95236800-95244600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr5:95236800-95260000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr5:95237800-95251800	Weak transcription	K562	blood
43	chr5:95238000-95243000	Weak transcription	Brain Angular Gyrus	brain
44	chr5:95238000-95243000	Weak transcription	Stomach Mucosa	stomach
45	chr5:95238000-95243200	Weak transcription	Brain Anterior Caudate	brain
46	chr5:95238000-95243200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:95238000-95243200	Weak transcription	HSMMtube	muscle
48	chr5:95238000-95244600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:95238000-95244600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:95238000-95244600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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