Variant report

Variant	rs2581470
Chromosome Location	chr15:100218867-100218868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1019974	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11247119	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12592092	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593522	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs12593785	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12595285	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12901291	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912791	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs12916000	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1434232	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap]
rs167805	0.87[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs170521	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs170522	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs188977	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs191256	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs2033546	0.84[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2117309	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2570807	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2570808	0.81[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2570816	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2570823	0.80[ASN][1000 genomes]
rs2570825	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2581467	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2581468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2581472	0.88[EUR][1000 genomes]
rs2862869	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2862870	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28712314	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2902349	0.93[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs325381	0.82[JPT][hapmap]
rs325390	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs325392	0.84[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs325394	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs325404	0.87[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs325409	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs325410	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs325413	0.94[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34443706	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34756251	0.97[ASN][1000 genomes]
rs34779575	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34981499	0.97[ASN][1000 genomes]
rs35410986	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35441914	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3730281	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3743180	0.81[YRI][hapmap]
rs4424892	0.80[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs4965529	0.89[ASN][1000 genomes]
rs4965532	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162392	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7165899	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs73482408	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7496677	0.94[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs892465	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs897073	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2581470	LYSMD4	cis	cerebellum	SCAN

Chromatin state (count:122 , 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	chr15:100171200-100232800	Weak transcription	Esophagus	oesophagus
3	chr15:100171200-100248800	Weak transcription	Gastric	stomach
4	chr15:100172000-100230800	Weak transcription	Stomach Mucosa	stomach
5	chr15:100179200-100232600	Weak transcription	Colonic Mucosa	Colon
6	chr15:100181800-100232800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:100190600-100222600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:100192000-100230400	Weak transcription	NHLF	lung
9	chr15:100193000-100229000	Weak transcription	Lung	lung
10	chr15:100199800-100232600	Weak transcription	Right Ventricle	heart
11	chr15:100200800-100221600	Weak transcription	Psoas Muscle	Psoas
12	chr15:100208400-100219200	Weak transcription	Small Intestine	intestine
13	chr15:100209800-100224400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:100209800-100232800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:100210800-100220600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:100210800-100223400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:100211000-100219800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr15:100211000-100219800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:100211600-100219600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr15:100211600-100220400	Strong transcription	Fetal Thymus	thymus
21	chr15:100211800-100219600	Strong transcription	Primary T cells from cord blood	blood
22	chr15:100211800-100219800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:100211800-100232200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:100212000-100221800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:100212800-100219200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:100212800-100223800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr15:100212800-100240000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:100213000-100232600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:100213200-100250800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:100213400-100221400	Weak transcription	Aorta	Aorta
31	chr15:100213400-100226400	Weak transcription	Fetal Brain Male	brain
32	chr15:100213400-100232600	Weak transcription	Pancreas	Pancrea
33	chr15:100213600-100243400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr15:100214400-100219600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:100214400-100219800	Strong transcription	NHDF-Ad	bronchial
36	chr15:100214400-100220400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:100214400-100220400	Strong transcription	Osteobl	bone
38	chr15:100214400-100220600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:100214400-100223200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr15:100214400-100223400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:100214400-100224200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:100214600-100219400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr15:100214600-100219400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:100214600-100219800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:100214600-100220400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:100214600-100220400	Strong transcription	Fetal Lung	lung
47	chr15:100215000-100224600	Strong transcription	Liver	Liver
48	chr15:100215600-100226400	Weak transcription	HepG2	liver
49	chr15:100215800-100219000	Weak transcription	A549	lung
50	chr15:100215800-100219200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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