Variant report

Variant	rs13362324
Chromosome Location	chr5:68580434-68580435
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68580179..68583024-chr5:68584330..68585895,2	K562	blood:
2	chr5:68558474..68560530-chr5:68578996..68581239,2	MCF-7	breast:
3	chr5:68578435..68581520-chr5:68628697..68631760,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215006	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10045526	0.94[ASN][1000 genomes]
rs10063757	0.88[ASN][1000 genomes]
rs10063969	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10471774	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10940209	0.81[EUR][1000 genomes]
rs10940210	0.85[EUR][1000 genomes]
rs12513817	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163444	0.81[CEU][hapmap]
rs164709	0.87[ASN][1000 genomes]
rs164789	0.87[ASN][1000 genomes]
rs171211	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2130757	0.81[EUR][1000 genomes]
rs2171148	0.80[EUR][1000 genomes]
rs2172056	0.81[EUR][1000 genomes]
rs2242350	0.88[ASN][1000 genomes]
rs2291519	0.81[EUR][1000 genomes]
rs2291520	0.81[EUR][1000 genomes]
rs28602964	0.81[EUR][1000 genomes]
rs28768211	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972366	0.80[EUR][1000 genomes]
rs34893396	0.88[ASN][1000 genomes]
rs350104	0.81[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs350106	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs350107	0.81[CEU][hapmap]
rs35308484	0.88[ASN][1000 genomes]
rs3890705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3934528	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4077460	0.90[EUR][1000 genomes]
rs426392	0.87[ASN][1000 genomes]
rs4266362	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4362903	0.85[EUR][1000 genomes]
rs4421064	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4541612	0.87[EUR][1000 genomes]
rs4629549	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60299793	0.86[ASN][1000 genomes]
rs62373164	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62373181	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62373187	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6450026	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450027	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676012	0.81[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs6866993	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6876783	0.81[EUR][1000 genomes]
rs693725	0.81[CEU][hapmap]
rs7733556	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13362324	MRPS36	cis	lymphoblastoid	seeQTL
rs13362324	CCDC125	cis	lung	GTEx
rs13362324	MRPS36	cis	multi-tissue	Pritchard
rs13362324	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs13362324	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531200-68584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
4	chr5:68550400-68581800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr5:68552000-68581200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:68552200-68580800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:68552200-68588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:68553000-68581400	Weak transcription	Psoas Muscle	Psoas
9	chr5:68553800-68587800	Weak transcription	Colonic Mucosa	Colon
10	chr5:68554200-68604400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:68559000-68583400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:68559200-68581200	Weak transcription	Fetal Kidney	kidney
13	chr5:68559600-68584000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:68562600-68584200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:68563000-68585200	Strong transcription	Liver	Liver
16	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
17	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr5:68566000-68591000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr5:68566800-68610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:68569400-68582000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:68571600-68581600	Strong transcription	Fetal Thymus	thymus
22	chr5:68573000-68587800	Weak transcription	Hela-S3	cervix
23	chr5:68573000-68590600	Weak transcription	HUVEC	blood vessel
24	chr5:68573200-68585600	Strong transcription	Fetal Intestine Small	intestine
25	chr5:68574000-68585000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:68574800-68581200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:68575400-68581600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:68575600-68584200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:68575600-68605000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:68575600-68608200	Weak transcription	Right Ventricle	heart
31	chr5:68576000-68583800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:68576000-68584200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr5:68576000-68605200	Weak transcription	Left Ventricle	heart
34	chr5:68576200-68584200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:68576200-68590600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:68576200-68605200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr5:68576200-68609400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:68576400-68581200	Weak transcription	GM12878-XiMat	blood
39	chr5:68576400-68581400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:68576400-68581600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:68576400-68581600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr5:68576400-68583800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:68576400-68583800	Weak transcription	Fetal Lung	lung
44	chr5:68576400-68584000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:68576400-68591000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:68576400-68593000	Weak transcription	HMEC	breast
47	chr5:68576400-68614400	Weak transcription	Colon Smooth Muscle	Colon
48	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
49	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:68576600-68582800	Weak transcription	Placenta Amnion	Placenta Amnion

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