Variant report

Variant	rs11949941
Chromosome Location	chr5:178296912-178296913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10039708	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11249599	0.81[EUR][1000 genomes]
rs11948175	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11948664	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11948690	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11949180	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949181	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11949892	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11950641	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11950746	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11952790	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11954382	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11955047	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11958804	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11958887	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11958941	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11960942	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12186577	0.80[EUR][1000 genomes]
rs12186584	0.81[EUR][1000 genomes]
rs12187167	0.81[EUR][1000 genomes]
rs12553	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1566106	0.89[EUR][1000 genomes]
rs35609799	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35957383	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56814168	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56872885	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56932649	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56951084	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57153194	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57426447	0.89[EUR][1000 genomes]
rs58354049	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58554591	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58672680	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58679434	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58941917	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59242428	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59736551	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59829327	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59849584	0.81[EUR][1000 genomes]
rs59994898	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60178472	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60277514	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60417551	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60601817	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60813042	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61295075	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61310482	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61492890	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61744382	0.81[EUR][1000 genomes]
rs6600991	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6859174	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6861717	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6863160	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6863202	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6863603	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6865216	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6866591	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6870926	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6877663	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6878353	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6882396	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6883566	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6887256	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6890083	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6894878	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6895371	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7706558	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7727497	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7729560	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7729717	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7731067	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178287600-178302400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr5:178288400-178299200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr5:178288600-178299400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:178288800-178297600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:178288800-178300000	Strong transcription	Fetal Lung	lung
7	chr5:178288800-178302200	Strong transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:178289000-178297000	Strong transcription	Fetal Stomach	stomach
10	chr5:178289000-178297400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:178289000-178297400	Strong transcription	Duodenum Mucosa	Duodenum
12	chr5:178289000-178299600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:178289000-178301000	Strong transcription	Fetal Muscle Leg	muscle
14	chr5:178289000-178301600	Weak transcription	Stomach Mucosa	stomach
15	chr5:178289200-178299000	Strong transcription	Fetal Brain Female	brain
16	chr5:178289400-178302200	Strong transcription	Brain Anterior Caudate	brain
17	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:178289800-178297200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:178289800-178297600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:178289800-178299000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:178289800-178300200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:178289800-178300200	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr5:178290000-178299400	Weak transcription	Fetal Heart	heart
24	chr5:178290000-178302200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:178290200-178297800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr5:178290600-178298600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:178290600-178298600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:178290600-178299000	Weak transcription	Fetal Brain Male	brain
29	chr5:178290600-178299600	Strong transcription	Brain Germinal Matrix	brain
30	chr5:178290600-178299800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:178290600-178301200	Strong transcription	Brain Cingulate Gyrus	brain
32	chr5:178290800-178298800	Strong transcription	Primary T cells from cord blood	blood
33	chr5:178290800-178300200	Strong transcription	Left Ventricle	heart
34	chr5:178291000-178298400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:178291000-178299200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:178291000-178299200	Strong transcription	Fetal Thymus	thymus
37	chr5:178291000-178300000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:178291200-178317400	ZNF genes & repeats	Liver	Liver
39	chr5:178291400-178298000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:178291400-178300200	Strong transcription	Dnd41	blood
41	chr5:178291600-178299000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:178291800-178299000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
43	chr5:178292000-178303000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:178292200-178299200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr5:178292200-178302200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr5:178292400-178297400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr5:178292600-178298600	Strong transcription	Brain Hippocampus Middle	brain
48	chr5:178292600-178299200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:178292600-178299400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr5:178292600-178299400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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