Variant report

Variant	rs2289558
Chromosome Location	chr15:99926440-99926441
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	chr15:99925089..99927995-chr15:99937922..99942440,4	K562	blood:

Variant related genes	Relation type
ENSG00000259760	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12148825	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1510059	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2136628	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs2602037	0.85[CHD][hapmap]
rs28651946	0.87[ASN][1000 genomes]
rs28729666	0.87[ASN][1000 genomes]
rs4471659	0.87[ASN][1000 genomes]
rs4545797	0.81[ASN][1000 genomes]
rs58762669	0.87[ASN][1000 genomes]
rs59136665	0.90[ASN][1000 genomes]
rs59855164	0.83[ASN][1000 genomes]
rs62023852	0.87[ASN][1000 genomes]
rs62023854	0.87[ASN][1000 genomes]
rs62023857	0.85[ASN][1000 genomes]
rs62023858	0.87[ASN][1000 genomes]
rs62025360	0.83[ASN][1000 genomes]
rs62025361	0.83[ASN][1000 genomes]
rs62025363	0.90[ASN][1000 genomes]
rs62025364	0.84[ASN][1000 genomes]
rs62025365	0.90[ASN][1000 genomes]
rs62025366	0.84[ASN][1000 genomes]
rs62025367	0.95[ASN][1000 genomes]
rs62025382	0.95[ASN][1000 genomes]
rs62025383	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6422002	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7167033	0.88[CHB][hapmap]
rs7181973	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs768159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8033188	1.00[CHB][hapmap]
rs8041236	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs978703	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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 target site	47 gene(s)	inside rSNPs	diseases
11	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2289558	LRRC28	cis	multi-tissue	Pritchard

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99867200-99926600	Weak transcription	NHEK	skin
2	chr15:99886600-99931400	Weak transcription	Esophagus	oesophagus
3	chr15:99903600-99926600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:99905000-99928200	Weak transcription	Pancreas	Pancrea
5	chr15:99907200-99926600	Weak transcription	Fetal Kidney	kidney
6	chr15:99907400-99928200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:99910400-99934400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:99915200-99947400	Weak transcription	Thymus	Thymus
9	chr15:99916800-99931200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:99923000-99927600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr15:99923000-99928400	Weak transcription	Brain Angular Gyrus	brain
12	chr15:99923200-99930800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:99923400-99927000	Weak transcription	Aorta	Aorta
14	chr15:99923400-99928600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:99923600-99927400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:99924200-99927400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:99924200-99928400	Weak transcription	Brain Substantia Nigra	brain
18	chr15:99924800-99926800	Enhancers	Right Atrium	heart
19	chr15:99924800-99926800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr15:99924800-99927000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:99924800-99927000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr15:99924800-99927000	Genic enhancers	Fetal Intestine Small	intestine
23	chr15:99924800-99927800	Enhancers	Ovary	ovary
24	chr15:99925000-99926800	Enhancers	Small Intestine	intestine
25	chr15:99925000-99926800	Genic enhancers	Dnd41	blood
26	chr15:99925000-99927000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:99925000-99927000	Enhancers	Primary T cells fromperipheralblood	blood
28	chr15:99925000-99927000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr15:99925000-99927400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:99925200-99926600	Enhancers	Rectal Smooth Muscle	rectum
31	chr15:99925200-99926800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:99925200-99926800	Enhancers	Colon Smooth Muscle	Colon
33	chr15:99925200-99926800	Enhancers	Fetal Heart	heart
34	chr15:99925200-99926800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr15:99925200-99927000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr15:99925200-99927000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr15:99925200-99927000	Enhancers	Liver	Liver
38	chr15:99925200-99927000	Enhancers	Left Ventricle	heart
39	chr15:99925200-99927000	Enhancers	Stomach Mucosa	stomach
40	chr15:99925200-99927600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr15:99925400-99926600	Flanking Active TSS	A549	lung
42	chr15:99925400-99926600	Enhancers	Osteobl	bone
43	chr15:99925400-99926800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr15:99925400-99926800	Enhancers	Right Ventricle	heart
45	chr15:99925400-99926800	Enhancers	NHLF	lung
46	chr15:99925400-99927000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:99925400-99927000	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr15:99925400-99927000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:99925400-99927000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr15:99925400-99927000	Enhancers	Fetal Lung	lung

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