Variant report

Variant	rs12913830
Chromosome Location	chr15:100234906-100234907
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:100234684..100235204-chr17:56708626..56709370,3	MCF-7	breast:
2	chr15:100234684..100235204-chr17:56708616..56709476,8	MCF-7	breast:
3	chr15:100233684..100235204-chr17:56706616..56709514,4	MCF-7	breast:
4	chr15:100234684..100235186-chr17:56708607..56709673,9	HCT-116	colon:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11247113	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11247118	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11247120	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12441844	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12591308	0.80[AMR][1000 genomes]
rs12593181	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901291	0.92[YRI][hapmap]
rs2033547	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2164058	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570808	0.81[ASW][hapmap]
rs28716652	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3743180	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4965533	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4965534	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4965536	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59812744	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62042267	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7163683	0.88[ASN][1000 genomes]
rs7176008	0.87[ASN][1000 genomes]
rs7178948	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];0.83[ASN][1000 genomes]
rs7179518	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7181767	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8024784	0.92[ASN][1000 genomes]
rs8030814	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8036535	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8037206	0.89[ASW][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	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
2	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
3	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
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904559	chr15:100174907-100255046	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv904562	chr15:100214935-100237682	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12913830	LYSMD4	cis	parietal	SCAN
rs12913830	LYSMD4	cis	cerebellum	SCAN
rs12913830	LYSMD4	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100159000-100253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:100171200-100248800	Weak transcription	Gastric	stomach
3	chr15:100212800-100240000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:100213200-100250800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:100213600-100243400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:100219400-100248200	Weak transcription	Small Intestine	intestine
7	chr15:100219600-100248400	Weak transcription	Spleen	Spleen
8	chr15:100219800-100243600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:100222800-100243600	Weak transcription	Brain Angular Gyrus	brain
10	chr15:100223600-100236600	Strong transcription	Fetal Lung	lung
11	chr15:100223600-100247400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:100223800-100241000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:100223800-100243600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:100223800-100246800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr15:100224000-100246600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:100226400-100236000	Strong transcription	Fetal Thymus	thymus
17	chr15:100226800-100240000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:100227000-100237200	Strong transcription	Primary B cells from cord blood	blood
19	chr15:100227000-100237600	Strong transcription	Primary B cells from peripheral blood	blood
20	chr15:100227200-100237000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:100227400-100235200	Strong transcription	HSMM	muscle
22	chr15:100227400-100237000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:100227400-100238200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:100227400-100238400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:100227600-100238600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:100227800-100238200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:100227800-100243600	Weak transcription	HepG2	liver
28	chr15:100228200-100237000	Strong transcription	Primary T cells from cord blood	blood
29	chr15:100228400-100238600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:100228800-100236600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr15:100228800-100238200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr15:100229000-100236400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:100229000-100237000	Strong transcription	Liver	Liver
34	chr15:100229000-100237600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:100229200-100236600	Strong transcription	Dnd41	blood
36	chr15:100229400-100236600	Strong transcription	NHDF-Ad	bronchial
37	chr15:100229600-100236000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr15:100229600-100236600	Strong transcription	Adipose Nuclei	Adipose
39	chr15:100229600-100237000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:100229600-100237600	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:100230000-100235000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:100230000-100235400	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr15:100230200-100235000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:100230200-100236800	Strong transcription	HMEC	breast
45	chr15:100230200-100237200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:100230400-100235400	Strong transcription	Fetal Intestine Large	intestine
47	chr15:100230400-100236600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr15:100230400-100237400	Strong transcription	Osteobl	bone
49	chr15:100230600-100237200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr15:100230600-100237800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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