Variant report

Variant	rs189849
Chromosome Location	chr5:52964065-52964066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10036570	0.82[ASN][1000 genomes]
rs10068241	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10471866	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10940322	0.85[EUR][1000 genomes]
rs10940323	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10940328	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10940330	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12514280	0.83[CHB][hapmap]
rs12654088	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13164833	0.82[ASN][1000 genomes]
rs13176154	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13177321	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13179304	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13190280	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1490769	0.91[CHB][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1532162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16881474	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs171740	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1844697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1873426	0.81[CEU][hapmap];0.91[JPT][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs189848	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs194364	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124950	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs256081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs256086	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256088	0.84[ASN][1000 genomes]
rs256092	0.86[ASN][1000 genomes]
rs256093	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256094	0.91[CHB][hapmap];0.91[ASN][1000 genomes]
rs256096	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs256098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256099	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256109	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256114	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs256115	0.83[ASN][1000 genomes]
rs256118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256119	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2607476	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2607477	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607482	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607483	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2607485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2607503	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2607510	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2636993	0.91[CHB][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs2637002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2637003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2637026	0.91[ASN][1000 genomes]
rs2637029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2655381	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3103597	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3103598	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3103600	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs3103601	0.83[ASN][1000 genomes]
rs3103602	0.84[ASN][1000 genomes]
rs3103899	0.83[ASN][1000 genomes]
rs31308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34071992	0.89[ASN][1000 genomes]
rs365358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs365578	0.91[CHB][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs365932	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs366313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs368461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs371123	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs372215	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs372370	0.87[ASN][1000 genomes]
rs377077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs377159	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs381575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs388311	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs392169	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs401967	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs402751	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs404838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs409313	0.85[ASN][1000 genomes]
rs412559	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs4147732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4147734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs417550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs425085	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs42565	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs425880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs426196	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs432020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs435713	0.87[CHB][hapmap];0.81[YRI][hapmap];0.87[ASN][1000 genomes]
rs438736	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs443254	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs444848	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs445347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449208	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs451591	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs451881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs454735	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4865547	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4865548	0.81[ASN][1000 genomes]
rs499760	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs524289	0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs535277	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs693204	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7717681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7736747	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs786330	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs786331	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs786334	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs918625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs923610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9292024	0.91[CHB][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs9687844	0.82[ASN][1000 genomes]
rs9790964	0.91[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52904400-52966600	Weak transcription	Osteobl	bone
2	chr5:52920800-52978800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:52929000-52981800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr5:52929400-52964600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:52935200-52978000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:52938200-52970200	Weak transcription	NH-A	brain
7	chr5:52938400-52967600	Weak transcription	Fetal Kidney	kidney
8	chr5:52938600-52971000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:52940000-52982000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:52941400-52980200	Weak transcription	HepG2	liver
11	chr5:52941400-52985200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:52942400-52973400	Weak transcription	Fetal Heart	heart
13	chr5:52944000-52969800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:52944200-52968200	Weak transcription	K562	blood
15	chr5:52945400-52974600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr5:52945400-52979000	Weak transcription	HMEC	breast
17	chr5:52945400-52980200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:52945400-52980800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr5:52945400-52981000	Weak transcription	Psoas Muscle	Psoas
20	chr5:52945400-52985000	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:52945600-52965400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:52945600-52971600	Weak transcription	Fetal Lung	lung
23	chr5:52945600-52978400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr5:52945600-52980800	Weak transcription	GM12878-XiMat	blood
25	chr5:52945600-52981600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:52945600-52983000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr5:52945600-52983600	Weak transcription	Fetal Thymus	thymus
28	chr5:52946800-52981400	Weak transcription	NHEK	skin
29	chr5:52955800-52964800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:52955800-52967200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:52955800-52982200	Weak transcription	Dnd41	blood
32	chr5:52956000-52965200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:52956000-52965200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:52956000-52982600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:52961200-52965600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr5:52961200-52974800	Weak transcription	HSMMtube	muscle
37	chr5:52961400-52970200	Weak transcription	Placenta	Placenta
38	chr5:52961600-52965400	Strong transcription	Primary B cells from cord blood	blood
39	chr5:52961600-52967000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:52961600-52967000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr5:52961600-52967600	Weak transcription	Thymus	Thymus
42	chr5:52961600-52975000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:52961600-52978800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr5:52961600-52984200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:52961800-52964600	Weak transcription	Fetal Intestine Small	intestine
46	chr5:52961800-52967600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr5:52961800-52968800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:52961800-52978200	Weak transcription	Left Ventricle	heart
49	chr5:52961800-52978800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr5:52961800-52979800	Weak transcription	Aorta	Aorta

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