Variant report

Variant	rs10039708
Chromosome Location	chr5:178292550-178292551
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178290096..178292803-chr5:178294356..178296794,2	K562	blood:

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

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

rs_ID	r²[population]
rs11249599	0.81[EUR][1000 genomes]
rs11948175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11948664	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11948690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11949180	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949181	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949892	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949941	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11950641	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11950746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11952790	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11954382	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11955047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11958804	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11958887	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11958941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11960942	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12553	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1566106	0.89[EUR][1000 genomes]
rs35609799	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35957383	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56814168	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56872885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56932649	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56951084	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57153194	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57426447	0.89[EUR][1000 genomes]
rs58354049	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58554591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58672680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58679434	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58941917	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59242428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59736551	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59829327	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59994898	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60178472	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60277514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60417551	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60601817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60813042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61295075	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61310482	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61492890	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6600991	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6859174	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6861717	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6863160	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6863202	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6863603	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6865216	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6866591	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6870926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6877663	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6878353	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6882396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6883566	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6887256	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6890083	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6894878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6895371	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7706558	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7727497	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7729560	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7729717	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7731067	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][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	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv462574	chr5:178269682-178313078	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv600463	chr5:178269682-178313078	Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv823352	chr5:178279625-178296623	Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178287600-178292600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:178287600-178294000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:178287600-178296200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:178287600-178302400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:178287800-178293200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:178288200-178295000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr5:178288400-178295000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr5:178288400-178295200	ZNF genes & repeats	A549	lung
10	chr5:178288400-178299200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr5:178288600-178293000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:178288600-178293000	Weak transcription	HSMMtube	muscle
13	chr5:178288600-178293200	Weak transcription	HUVEC	blood vessel
14	chr5:178288600-178299400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:178288800-178292600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:178288800-178292800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:178288800-178293000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:178288800-178293000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:178288800-178293400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:178288800-178294800	Strong transcription	HSMM	muscle
21	chr5:178288800-178296000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr5:178288800-178297600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:178288800-178300000	Strong transcription	Fetal Lung	lung
24	chr5:178288800-178302200	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:178289000-178292600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:178289000-178292800	Weak transcription	Fetal Kidney	kidney
28	chr5:178289000-178293000	Weak transcription	Colonic Mucosa	Colon
29	chr5:178289000-178293000	Weak transcription	Small Intestine	intestine
30	chr5:178289000-178293600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:178289000-178295000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:178289000-178297000	Strong transcription	Fetal Stomach	stomach
33	chr5:178289000-178297400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:178289000-178297400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr5:178289000-178299600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:178289000-178301000	Strong transcription	Fetal Muscle Leg	muscle
37	chr5:178289000-178301600	Weak transcription	Stomach Mucosa	stomach
38	chr5:178289200-178293000	Weak transcription	Brain Angular Gyrus	brain
39	chr5:178289200-178299000	Strong transcription	Fetal Brain Female	brain
40	chr5:178289400-178293600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:178289400-178302200	Strong transcription	Brain Anterior Caudate	brain
42	chr5:178289600-178294800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:178289600-178295400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr5:178289800-178292800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:178289800-178293000	Weak transcription	Gastric	stomach
47	chr5:178289800-178297200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:178289800-178297600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:178289800-178299000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:178289800-178300200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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