Variant report

Variant	rs28390247
Chromosome Location	chr4:88127028-88127029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88125915..88129051-chr4:88140439..88142912,3	MCF-7	breast:
2	chr4:88122608..88124164-chr4:88126529..88128158,2	K562	blood:

Variant related genes	Relation type
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10049549	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12710836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13105620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13126252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13134294	0.84[AMR][1000 genomes]
rs13134907	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13140294	0.84[AMR][1000 genomes]
rs13145898	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13435811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17704256	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17755195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2035404	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2054611	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28523549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28621526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28655413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28668976	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28773027	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34128785	0.84[AMR][1000 genomes]
rs34242006	0.84[AMR][1000 genomes]
rs34422965	0.84[AMR][1000 genomes]
rs34589806	0.84[AMR][1000 genomes]
rs35133616	0.84[AMR][1000 genomes]
rs35542725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36123985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71607405	0.80[AMR][1000 genomes]
rs71607410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999554	1.00[AMR][1000 genomes];1.00[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	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28390247	KLHL8	cis	multi-tissue	Pritchard
rs28390247	MAPKAPK5	trans	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88081800-88140200	Weak transcription	Aorta	Aorta
2	chr4:88082000-88129200	Weak transcription	Esophagus	oesophagus
3	chr4:88085000-88128000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:88089600-88131000	Weak transcription	Ovary	ovary
5	chr4:88091800-88128000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:88091800-88128600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:88091800-88133600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:88092200-88134800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:88097600-88140400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:88098000-88127400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:88109600-88133600	Weak transcription	Fetal Lung	lung
12	chr4:88110400-88127600	Weak transcription	Liver	Liver
13	chr4:88110800-88128200	Weak transcription	Fetal Intestine Small	intestine
14	chr4:88114600-88129000	Weak transcription	K562	blood
15	chr4:88115400-88128000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr4:88115800-88131000	Weak transcription	Gastric	stomach
17	chr4:88116400-88138000	Weak transcription	HepG2	liver
18	chr4:88118800-88127600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:88119400-88132600	Weak transcription	Psoas Muscle	Psoas
20	chr4:88121200-88128400	Weak transcription	Right Ventricle	heart
21	chr4:88121200-88130400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr4:88121200-88134600	Weak transcription	Pancreas	Pancrea
23	chr4:88122400-88140000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:88123600-88127800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:88124400-88128200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:88124600-88127600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:88124800-88128000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:88124800-88128000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:88124800-88129400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr4:88125400-88127200	Weak transcription	Primary B cells from cord blood	blood
31	chr4:88125400-88134600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:88125400-88134800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:88125400-88140200	Weak transcription	Fetal Intestine Large	intestine
34	chr4:88125600-88127600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr4:88125600-88128000	Weak transcription	Primary T cells from cord blood	blood
36	chr4:88125600-88130200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:88125600-88134600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:88125800-88134600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr4:88126000-88132800	Weak transcription	Fetal Heart	heart
40	chr4:88126200-88128200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:88126600-88128000	Weak transcription	Brain Germinal Matrix	brain
42	chr4:88126600-88128200	Weak transcription	Spleen	Spleen
43	chr4:88126600-88128600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:88126800-88130400	Weak transcription	Adipose Nuclei	Adipose
45	chr4:88126800-88130400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:88126800-88140000	Weak transcription	Fetal Stomach	stomach

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