Variant report

Variant	rs12912791
Chromosome Location	chr15:100158444-100158445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1019974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11247119	0.86[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs12592092	0.91[ASN][1000 genomes]
rs12593522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593785	0.91[ASN][1000 genomes]
rs12595285	0.86[ASN][1000 genomes]
rs12901291	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12916000	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs1434232	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs167805	0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs170521	0.91[ASN][1000 genomes]
rs170522	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs188977	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs191256	0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs2033546	0.86[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs2117309	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2570807	0.82[ASN][1000 genomes]
rs2570808	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2570816	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570823	0.80[ASN][1000 genomes]
rs2570825	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2581467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2581468	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2581470	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]
rs28712314	0.88[ASN][1000 genomes]
rs2902349	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs325381	0.82[JPT][hapmap]
rs325390	0.91[ASN][1000 genomes]
rs325392	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs325394	0.92[ASN][1000 genomes]
rs325404	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs325409	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs325410	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs325413	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs34443706	0.86[ASN][1000 genomes]
rs34756251	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34779575	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34981499	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35410986	0.91[ASN][1000 genomes]
rs35441914	0.95[ASN][1000 genomes]
rs3730281	0.91[ASN][1000 genomes]
rs4424892	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs4965529	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4965532	0.97[ASN][1000 genomes]
rs7162392	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7165899	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs73482408	0.91[ASN][1000 genomes]
rs7496677	0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.80[ASN][1000 genomes]
rs892465	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs897073	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv904558	chr15:100019382-100171684	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12912791	LYSMD4	cis	cerebellum	SCAN
rs12912791	LYSMD4	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100133000-100159200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:100133000-100159200	Weak transcription	A549	lung
3	chr15:100142600-100159200	Weak transcription	Gastric	stomach
4	chr15:100142800-100159200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:100142800-100159400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr15:100142800-100164000	Weak transcription	Fetal Thymus	thymus
7	chr15:100142800-100176400	Weak transcription	Fetal Stomach	stomach
8	chr15:100143000-100163200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:100143800-100159200	Weak transcription	Lung	lung
10	chr15:100144000-100159200	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:100144000-100180800	Weak transcription	Thymus	Thymus
12	chr15:100145600-100159200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:100146200-100159200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:100148600-100159200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:100150800-100159200	Weak transcription	HSMM	muscle
16	chr15:100153000-100158600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr15:100153200-100160400	Enhancers	Liver	Liver
18	chr15:100153400-100159000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:100153400-100159400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr15:100154000-100159600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:100155000-100159400	Weak transcription	Hela-S3	cervix
22	chr15:100155200-100159200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:100155200-100159200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:100155200-100159200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:100155200-100159200	Weak transcription	Colonic Mucosa	Colon
26	chr15:100155200-100159200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:100155200-100159200	Weak transcription	Pancreas	Pancrea
28	chr15:100155200-100159200	Weak transcription	NHLF	lung
29	chr15:100155200-100160600	Enhancers	Fetal Heart	heart
30	chr15:100155200-100163600	Weak transcription	Dnd41	blood
31	chr15:100155200-100191000	Weak transcription	HSMMtube	muscle
32	chr15:100155400-100158800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:100155400-100158800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:100155400-100159000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:100155400-100159200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:100155400-100159200	Weak transcription	Esophagus	oesophagus
37	chr15:100155400-100159200	Weak transcription	Placenta	Placenta
38	chr15:100155400-100159400	Weak transcription	Small Intestine	intestine
39	chr15:100155400-100164200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr15:100155400-100168400	Weak transcription	Stomach Mucosa	stomach
41	chr15:100155400-100170800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr15:100155400-100180800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:100155600-100158600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:100155600-100159200	Weak transcription	Aorta	Aorta
45	chr15:100155600-100164200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:100156000-100159200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr15:100156000-100159200	Weak transcription	Fetal Intestine Small	intestine
48	chr15:100156000-100159200	Weak transcription	Left Ventricle	heart
49	chr15:100156000-100159200	Weak transcription	Ovary	ovary
50	chr15:100156000-100159200	Weak transcription	Psoas Muscle	Psoas

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