Variant report

Variant	rs9999554
Chromosome Location	chr4:88110057-88110058
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	chr4:88109467..88112377-chr4:88113145..88115434,2	K562	blood:
2	chr4:88109625..88111275-chr4:88140234..88142078,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145332	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10049549	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12710836	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13105620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13126252	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13134294	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs13134907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13140294	0.84[AMR][1000 genomes]
rs13142380	1.00[AFR][1000 genomes]
rs13143182	1.00[AFR][1000 genomes]
rs13145898	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13435811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17704256	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17755195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2035404	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2054611	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28390247	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28523549	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28621526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28655413	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	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs34422965	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs34589806	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35133616	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs35534149	1.00[AFR][1000 genomes]
rs35542725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36123985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71607405	0.80[AMR][1000 genomes]
rs71607407	1.00[AFR][1000 genomes]
rs71607410	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
rs9999554	KLHL8	cis	multi-tissue	Pritchard
rs9999554	MAPKAPK5	trans	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88068000-88116400	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr4:88073400-88113000	Weak transcription	NHDF-Ad	bronchial
3	chr4:88077200-88111000	Weak transcription	Fetal Brain Male	brain
4	chr4:88081800-88140200	Weak transcription	Aorta	Aorta
5	chr4:88082000-88111000	Weak transcription	Brain Germinal Matrix	brain
6	chr4:88082000-88129200	Weak transcription	Esophagus	oesophagus
7	chr4:88082600-88120000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:88083000-88116400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:88084800-88113600	Weak transcription	HSMM	muscle
10	chr4:88085000-88128000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:88089600-88113600	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:88089600-88131000	Weak transcription	Ovary	ovary
13	chr4:88089800-88115800	Weak transcription	HepG2	liver
14	chr4:88090000-88118200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:88091200-88111600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:88091400-88118200	Weak transcription	Brain Anterior Caudate	brain
17	chr4:88091800-88115000	Weak transcription	Left Ventricle	heart
18	chr4:88091800-88128000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:88091800-88128600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:88091800-88133600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:88092200-88134800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:88093000-88113200	Weak transcription	K562	blood
23	chr4:88093800-88113400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:88093800-88119600	Weak transcription	Primary T cells from cord blood	blood
25	chr4:88096800-88115400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:88097600-88110200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:88097600-88125200	Weak transcription	Primary B cells from cord blood	blood
28	chr4:88097600-88140400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:88098000-88114800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:88098000-88127400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:88098400-88110200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:88098800-88115600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:88099000-88118400	Weak transcription	Fetal Intestine Large	intestine
34	chr4:88099200-88110200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:88099800-88115200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:88100400-88119200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr4:88102400-88110600	Weak transcription	Fetal Intestine Small	intestine
38	chr4:88106800-88110200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:88106800-88113000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:88107000-88112800	Weak transcription	GM12878-XiMat	blood
41	chr4:88108600-88115600	Weak transcription	Gastric	stomach
42	chr4:88109200-88110400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:88109400-88110400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:88109600-88110400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr4:88109600-88133600	Weak transcription	Fetal Lung	lung
46	chr4:88109800-88110400	Active TSS	Liver	Liver
47	chr4:88110000-88110200	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr4:88110000-88110400	Weak transcription	Lung	lung
49	chr4:88110000-88110400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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