Variant report

Variant	rs28373740
Chromosome Location	chr5:112085611-112085612
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112071994..112074935-chr5:112084057..112088000,3	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10051624	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10071425	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10075281	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10075323	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10075377	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10213844	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10477483	0.81[AMR][1000 genomes]
rs11241183	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11241184	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11241185	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11749701	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12332692	0.81[AMR][1000 genomes]
rs12513787	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12518091	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12658609	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12659119	0.80[EUR][1000 genomes]
rs13156251	0.81[AMR][1000 genomes]
rs1914	0.85[AMR][1000 genomes]
rs1974786	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2019720	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2251913	0.84[AMR][1000 genomes]
rs2253987	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2289484	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2431239	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2431241	0.85[AMR][1000 genomes]
rs2431512	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2439589	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2464803	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2545158	0.85[AMR][1000 genomes]
rs2546106	0.85[AMR][1000 genomes]
rs2546107	0.83[AMR][1000 genomes]
rs2546108	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2546117	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707763	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2707765	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28578275	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2901844	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs351772	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35414976	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs390092	0.85[AMR][1000 genomes]
rs414098	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs458906	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs467033	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4705486	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4705559	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4705573	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4705608	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4705610	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4705624	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs511906	0.84[AMR][1000 genomes]
rs518013	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs548710	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62364017	0.81[EUR][1000 genomes]
rs6594646	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6862050	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6864688	0.81[EUR][1000 genomes]
rs6879057	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7704618	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7727738	0.81[AMR][1000 genomes]
rs9647582	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9647583	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112073800-112086800	Weak transcription	Gastric	stomach
2	chr5:112074000-112095000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:112074200-112093200	Weak transcription	Aorta	Aorta
4	chr5:112074400-112090400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr5:112074400-112090400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr5:112074400-112091000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:112074400-112093200	Weak transcription	Right Ventricle	heart
8	chr5:112074400-112094000	Weak transcription	Fetal Intestine Small	intestine
9	chr5:112074400-112095200	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:112074400-112095600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr5:112074400-112095600	Weak transcription	Fetal Thymus	thymus
12	chr5:112074400-112095800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:112074400-112102800	Weak transcription	Fetal Stomach	stomach
14	chr5:112074400-112103400	Weak transcription	Left Ventricle	heart
15	chr5:112074400-112119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:112074400-112125600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:112074400-112128600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:112074600-112090400	Weak transcription	Primary B cells from cord blood	blood
19	chr5:112074600-112103000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:112074800-112097600	Weak transcription	HMEC	breast
21	chr5:112075000-112093000	Weak transcription	Liver	Liver
22	chr5:112075000-112095200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:112075200-112092600	Weak transcription	HSMM	muscle
24	chr5:112075200-112094400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:112075200-112103000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:112075400-112091000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:112075400-112097400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:112075400-112101600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:112075600-112095600	Weak transcription	Dnd41	blood
30	chr5:112075600-112095800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:112076000-112090800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr5:112076000-112095400	Weak transcription	NH-A	brain
33	chr5:112076200-112097000	Weak transcription	NHLF	lung
34	chr5:112078000-112095800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:112078400-112091200	Weak transcription	Primary T cells from cord blood	blood
36	chr5:112078600-112093000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:112078600-112095800	Weak transcription	GM12878-XiMat	blood
38	chr5:112078800-112092000	Weak transcription	Fetal Brain Male	brain
39	chr5:112078800-112097200	Weak transcription	NHDF-Ad	bronchial
40	chr5:112079000-112090600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:112079600-112086000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:112079600-112128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr5:112079800-112095600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr5:112079800-112128600	Weak transcription	Small Intestine	intestine
45	chr5:112080000-112089200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr5:112080200-112089200	Weak transcription	Brain Substantia Nigra	brain
47	chr5:112080200-112090600	Weak transcription	Fetal Brain Female	brain
48	chr5:112080200-112095800	Weak transcription	K562	blood
49	chr5:112080800-112088200	Weak transcription	Brain Anterior Caudate	brain
50	chr5:112081200-112128600	Weak transcription	H9 Cell Line	embryonic stem cell

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