Variant report

Variant	rs2829
Chromosome Location	chr5:95258447-95258448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95257637..95262263-chr5:95295485..95300660,6	K562	blood:
2	chr5:95257088..95259810-chr5:95296107..95298833,3	K562	blood:
3	chr5:95252395..95254365-chr5:95256806..95259702,2	MCF-7	breast:
4	chr5:95256084..95258584-chr5:95264436..95266158,3	K562	blood:

Variant related genes	Relation type
ENSG00000118985	Chromatin interaction
ENSG00000251314	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10035477	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10069748	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10070197	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1043381	0.95[EUR][1000 genomes]
rs1057963	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1057964	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11135442	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11738768	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11739652	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11741563	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11741590	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11744881	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13361341	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13361837	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1423268	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1423269	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458017	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1458018	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1458019	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs147295	0.81[EUR][1000 genomes]
rs17085231	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17085249	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17085266	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1841010	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2015159	0.94[EUR][1000 genomes]
rs2042340	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270554	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2348984	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2546191	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547997	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548594	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777182	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777183	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777184	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777185	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777188	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777189	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777190	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777192	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777193	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777194	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777196	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777197	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777200	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777201	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777202	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777203	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777204	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777208	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3815768	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4563648	0.94[EUR][1000 genomes]
rs4642392	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56156268	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56219066	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6556893	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6877329	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6879652	0.95[EUR][1000 genomes]
rs6885567	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6889029	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6890954	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7702674	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7716691	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs889302	0.94[EUR][1000 genomes]
rs9314162	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967546	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9986236	0.97[EUR][1000 genomes];0.87[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:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95223000-95259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:95226400-95263600	Weak transcription	Colonic Mucosa	Colon
3	chr5:95236400-95276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:95236800-95260000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:95238200-95260400	Weak transcription	A549	lung
6	chr5:95238200-95282000	Weak transcription	HUVEC	blood vessel
7	chr5:95242600-95259000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:95242600-95259800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:95243400-95278800	Weak transcription	Lung	lung
10	chr5:95243600-95274200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:95244400-95258600	Weak transcription	Fetal Intestine Large	intestine
12	chr5:95244800-95260600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:95245200-95259000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:95246400-95266400	Weak transcription	NHDF-Ad	bronchial
15	chr5:95249800-95271600	Weak transcription	NH-A	brain
16	chr5:95250600-95263000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr5:95251200-95259000	Weak transcription	Fetal Intestine Small	intestine
18	chr5:95251200-95260200	Genic enhancers	Liver	Liver
19	chr5:95251200-95261800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:95251400-95260200	Genic enhancers	HepG2	liver
21	chr5:95251600-95259000	Weak transcription	Stomach Mucosa	stomach
22	chr5:95251800-95259000	Weak transcription	Right Ventricle	heart
23	chr5:95252000-95258600	Weak transcription	NHLF	lung
24	chr5:95252200-95263800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:95252200-95272400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:95252400-95259000	Weak transcription	Psoas Muscle	Psoas
27	chr5:95252400-95259600	Weak transcription	Fetal Thymus	thymus
28	chr5:95252400-95260400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:95252400-95260600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:95252400-95264600	Weak transcription	Ovary	ovary
31	chr5:95252400-95266400	Weak transcription	HSMMtube	muscle
32	chr5:95252600-95259400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr5:95253000-95258600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:95253200-95259200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:95253400-95258600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:95253400-95259000	Weak transcription	Adipose Nuclei	Adipose
37	chr5:95253400-95259600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr5:95253400-95259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:95253400-95262600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:95253800-95272400	Weak transcription	Placenta	Placenta
41	chr5:95254600-95258600	Weak transcription	K562	blood
42	chr5:95254600-95258800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr5:95254600-95259000	Weak transcription	Small Intestine	intestine
44	chr5:95254600-95259000	Weak transcription	Dnd41	blood
45	chr5:95254600-95266000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:95254800-95258600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:95254800-95259000	Weak transcription	Brain Angular Gyrus	brain
48	chr5:95255200-95259000	Weak transcription	Primary B cells from cord blood	blood
49	chr5:95255400-95259000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr5:95256200-95259400	Enhancers	Gastric	stomach

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