Variant report

Variant	rs171790
Chromosome Location	chr5:89816299-89816300
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89768184..89771456-chr5:89815770..89820278,7	K562	blood:
2	chr5:89801454..89803110-chr5:89815807..89818860,3	K562	blood:
3	chr5:89801341..89803372-chr5:89815675..89817477,2	MCF-7	breast:
4	chr5:89815006..89818203-chr5:89822291..89825301,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10069050	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154568	0.89[EUR][1000 genomes]
rs154569	0.89[EUR][1000 genomes]
rs154570	0.90[EUR][1000 genomes]
rs154572	0.84[EUR][1000 genomes]
rs154573	0.85[EUR][1000 genomes]
rs1553545	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs250377	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257850	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257851	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656957	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27201	0.91[EUR][1000 genomes]
rs37238	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37239	0.83[EUR][1000 genomes]
rs37240	0.83[EUR][1000 genomes]
rs42467	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs43149	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs491082	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511393	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs526806	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs556894	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59159252	0.82[ASN][1000 genomes]
rs594990	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs599432	0.87[EUR][1000 genomes]
rs679568	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6884154	0.81[EUR][1000 genomes]
rs810974	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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
rs171790	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	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:89793800-89823400	Weak transcription	Hela-S3	cervix
4	chr5:89797600-89824200	Weak transcription	Brain Angular Gyrus	brain
5	chr5:89799600-89817200	Weak transcription	NHDF-Ad	bronchial
6	chr5:89802600-89824600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:89803200-89817600	Weak transcription	Small Intestine	intestine
8	chr5:89804000-89816400	Weak transcription	Thymus	Thymus
9	chr5:89805600-89819800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:89805600-89823200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:89805800-89819800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:89806400-89818200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:89808800-89822000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:89809000-89817000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:89809000-89817200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:89809000-89817800	Weak transcription	Brain Anterior Caudate	brain
17	chr5:89809000-89824000	Weak transcription	Right Ventricle	heart
18	chr5:89809000-89824400	Weak transcription	Psoas Muscle	Psoas
19	chr5:89809200-89816400	Weak transcription	Fetal Stomach	stomach
20	chr5:89809200-89824600	Weak transcription	Spleen	Spleen
21	chr5:89809600-89822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:89810000-89822200	Weak transcription	Fetal Heart	heart
23	chr5:89810000-89822400	Weak transcription	Fetal Intestine Small	intestine
24	chr5:89810200-89822000	Weak transcription	Stomach Mucosa	stomach
25	chr5:89810400-89822000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:89810400-89822800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:89810600-89824400	Weak transcription	Lung	lung
28	chr5:89810800-89817800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:89810800-89824400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:89810800-89824400	Weak transcription	Esophagus	oesophagus
31	chr5:89811000-89820400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:89811000-89824000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:89811000-89824400	Weak transcription	Pancreas	Pancrea
34	chr5:89811400-89821200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr5:89812000-89821000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr5:89812000-89821200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr5:89812200-89817600	Strong transcription	HSMM	muscle
38	chr5:89812200-89822000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:89812600-89822400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:89813000-89823400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr5:89813200-89820200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:89813400-89819600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr5:89813400-89821200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr5:89813400-89821200	Strong transcription	Fetal Intestine Large	intestine
45	chr5:89813400-89821600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:89813400-89822200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr5:89813400-89822800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:89813400-89824200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:89813400-89824400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:89813600-89821800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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