Variant report

Variant	rs28806288
Chromosome Location	chr4:151048211-151048212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151043515..151045552-chr4:151046673..151048620,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10003178	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10004630	0.91[AFR][1000 genomes]
rs10005992	0.81[AFR][1000 genomes]
rs10011368	0.91[AFR][1000 genomes]
rs10014266	0.91[AFR][1000 genomes]
rs10018922	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10022936	0.91[AFR][1000 genomes]
rs10026506	0.91[AFR][1000 genomes]
rs10027662	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10031412	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13435543	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28360726	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28374205	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28392881	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28397206	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28413051	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28416593	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs28423983	0.91[AFR][1000 genomes]
rs28439804	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28513621	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28559901	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28605560	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28642700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28654919	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28665284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28714207	0.81[ASN][1000 genomes]
rs28735454	0.91[AFR][1000 genomes]
rs28887006	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28896206	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4259040	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4339189	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4356899	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4423856	0.91[AFR][1000 genomes]
rs4459971	0.84[AFR][1000 genomes]
rs4631016	0.91[AFR][1000 genomes]
rs56150320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57168672	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60160057	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs61361070	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62338190	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62339860	0.91[AFR][1000 genomes]
rs62339861	0.91[AFR][1000 genomes]
rs62339874	0.91[AFR][1000 genomes]
rs62339875	0.91[AFR][1000 genomes]
rs62339876	0.91[AFR][1000 genomes]
rs62339877	0.91[AFR][1000 genomes]
rs62339878	0.91[AFR][1000 genomes]
rs62339880	0.91[AFR][1000 genomes]
rs62339909	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6848344	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659009	0.91[AFR][1000 genomes]
rs9307863	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9784426	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9968348	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9968351	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9985766	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9992748	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28806288	LRBA	Cis_1M	lymphoblastoid	RTeQTL
rs28806288	DCLK2	cis	Whole Blood	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151037400-151048400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:151038200-151051600	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:151038800-151070000	Weak transcription	Ovary	ovary
4	chr4:151039000-151048600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:151039000-151052800	Weak transcription	Right Ventricle	heart
6	chr4:151043200-151048800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:151043200-151052200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:151043400-151051600	Weak transcription	Brain Substantia Nigra	brain
9	chr4:151044200-151052800	Weak transcription	Brain Germinal Matrix	brain
10	chr4:151044600-151049400	Enhancers	Primary B cells from peripheral blood	blood
11	chr4:151044800-151049000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:151045200-151099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:151045400-151052800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:151046600-151049000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr4:151046800-151048400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr4:151047200-151048400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:151047200-151048400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:151047200-151048600	Enhancers	HUVEC	blood vessel
19	chr4:151047200-151049600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:151047200-151049600	Enhancers	NHDF-Ad	bronchial
21	chr4:151047200-151049800	Enhancers	NHLF	lung
22	chr4:151047200-151050000	Enhancers	HSMMtube	muscle
23	chr4:151047200-151050200	Enhancers	HSMM	muscle
24	chr4:151047200-151050400	Enhancers	Osteobl	bone
25	chr4:151047400-151048400	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr4:151047400-151049200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:151047400-151049200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:151047400-151049400	Enhancers	NHEK	skin
29	chr4:151047400-151058200	Weak transcription	Left Ventricle	heart
30	chr4:151047600-151049200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:151047800-151049000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr4:151047800-151049200	Enhancers	HMEC	breast
33	chr4:151047800-151051600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:151048000-151049200	Enhancers	Brain Cingulate Gyrus	brain
35	chr4:151048000-151050400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:151048200-151048600	Weak transcription	Brain Anterior Caudate	brain
37	chr4:151048200-151049000	Enhancers	GM12878-XiMat	blood
38	chr4:151048200-151049400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:151048200-151049600	Weak transcription	Fetal Heart	heart
40	chr4:151048200-151050400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr4:151048200-151050400	Enhancers	NH-A	brain
42	chr4:151048200-151050600	Enhancers	A549	lung
43	chr4:151048200-151051800	Weak transcription	Colon Smooth Muscle	Colon

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