Variant report

Variant	rs790081
Chromosome Location	chr5:89815761-89815762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10069050	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1553545	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs171790	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2255938	0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs250372	0.88[EUR][1000 genomes]
rs250373	0.88[EUR][1000 genomes]
rs250374	0.87[EUR][1000 genomes]
rs250375	0.88[EUR][1000 genomes]
rs250377	0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs257850	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs257851	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2656957	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs27198	0.90[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs27963	0.91[EUR][1000 genomes]
rs37238	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs42467	0.83[CHD][hapmap]
rs43149	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4569906	0.87[EUR][1000 genomes]
rs491082	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs511393	0.86[CHB][hapmap];0.91[CHD][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs526806	0.91[ASN][1000 genomes]
rs556894	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs59159252	0.82[ASN][1000 genomes]
rs594990	0.87[ASN][1000 genomes]
rs679568	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs6877680	0.88[EUR][1000 genomes]
rs810974	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs812594	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs790081	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89773800-89816000	Weak transcription	HepG2	liver
2	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:89793800-89823400	Weak transcription	Hela-S3	cervix
5	chr5:89797600-89824200	Weak transcription	Brain Angular Gyrus	brain
6	chr5:89799600-89817200	Weak transcription	NHDF-Ad	bronchial
7	chr5:89802600-89824600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:89803200-89817600	Weak transcription	Small Intestine	intestine
9	chr5:89804000-89816400	Weak transcription	Thymus	Thymus
10	chr5:89805600-89819800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:89805600-89823200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:89805800-89819800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:89806400-89818200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:89808800-89816000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr5:89808800-89822000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:89809000-89817000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr5:89809000-89817200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:89809000-89817800	Weak transcription	Brain Anterior Caudate	brain
19	chr5:89809000-89824000	Weak transcription	Right Ventricle	heart
20	chr5:89809000-89824400	Weak transcription	Psoas Muscle	Psoas
21	chr5:89809200-89816400	Weak transcription	Fetal Stomach	stomach
22	chr5:89809200-89824600	Weak transcription	Spleen	Spleen
23	chr5:89809600-89822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:89810000-89822200	Weak transcription	Fetal Heart	heart
25	chr5:89810000-89822400	Weak transcription	Fetal Intestine Small	intestine
26	chr5:89810200-89822000	Weak transcription	Stomach Mucosa	stomach
27	chr5:89810400-89822000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:89810400-89822800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:89810600-89816000	Weak transcription	Aorta	Aorta
30	chr5:89810600-89824400	Weak transcription	Lung	lung
31	chr5:89810800-89817800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:89810800-89824400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:89810800-89824400	Weak transcription	Esophagus	oesophagus
34	chr5:89811000-89820400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:89811000-89824000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:89811000-89824400	Weak transcription	Pancreas	Pancrea
37	chr5:89811400-89815800	Weak transcription	Brain Hippocampus Middle	brain
38	chr5:89811400-89821200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr5:89812000-89821000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr5:89812000-89821200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr5:89812200-89817600	Strong transcription	HSMM	muscle
42	chr5:89812200-89822000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:89812600-89822400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:89813000-89816000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr5:89813000-89823400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:89813200-89816000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:89813200-89820200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:89813400-89819600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr5:89813400-89821200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr5:89813400-89821200	Strong transcription	Fetal Intestine Large	intestine

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