Variant report

Variant	rs13054238
Chromosome Location	chr22:30620891-30620892
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	chr22:30619180..30621137-chr22:30621578..30624236,2	K562	blood:
2	chr22:30619504..30622995-chr22:30623297..30627180,5	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11089441	0.89[ASW][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap]
rs11089442	1.00[LWK][hapmap]
rs11704358	1.00[LWK][hapmap]
rs1557833	0.91[ASN][1000 genomes]
rs2073946	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2267153	0.91[CHB][hapmap]
rs2839998	1.00[LWK][hapmap]
rs3753082	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3761427	0.91[CHB][hapmap];0.84[AFR][1000 genomes]
rs8141656	1.00[LWK][hapmap]
rs929271	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs929272	0.95[CEU][hapmap]
rs929273	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9606708	0.89[ASW][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.83[MEX][hapmap];0.84[AFR][1000 genomes]
rs9619096	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv914969	chr22:30619599-30691631	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13054238	LRP5L	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30605600-30622600	Weak transcription	Right Atrium	heart
2	chr22:30611200-30624800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:30614400-30624800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:30615400-30626000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr22:30615600-30627000	Weak transcription	K562	blood
6	chr22:30616000-30621000	Enhancers	Primary B cells from cord blood	blood
7	chr22:30617400-30621800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr22:30617400-30624000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr22:30617600-30622000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr22:30617800-30621800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr22:30618000-30622600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr22:30618000-30623600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr22:30618000-30625000	Weak transcription	Esophagus	oesophagus
14	chr22:30618200-30621000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr22:30618200-30623600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr22:30618400-30621200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr22:30618600-30622800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr22:30619000-30621200	Enhancers	Primary B cells from peripheral blood	blood
19	chr22:30619000-30622200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr22:30619200-30621000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr22:30619200-30621000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr22:30619200-30621000	Enhancers	Osteobl	bone
23	chr22:30619200-30621200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr22:30619200-30621200	Enhancers	NH-A	brain
25	chr22:30619200-30622000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr22:30619200-30625600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr22:30619400-30621000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr22:30619400-30621000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr22:30619600-30621000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr22:30619600-30621000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr22:30619600-30621400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr22:30619600-30622400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr22:30619600-30625800	Enhancers	HMEC	breast
34	chr22:30619800-30622800	Weak transcription	Spleen	Spleen
35	chr22:30619800-30625600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr22:30620000-30621000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:30620000-30621000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr22:30620000-30621000	Enhancers	HSMM	muscle
39	chr22:30620000-30621000	Enhancers	HSMMtube	muscle
40	chr22:30620000-30622200	Enhancers	NHEK	skin
41	chr22:30620000-30625600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr22:30620200-30621000	Enhancers	GM12878-XiMat	blood
43	chr22:30620200-30623600	Weak transcription	Fetal Thymus	thymus
44	chr22:30620400-30621000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr22:30620400-30621800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr22:30620600-30622200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr22:30620600-30622400	Enhancers	Dnd41	blood
48	chr22:30620600-30623600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr22:30620600-30624000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr22:30620600-30624600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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