Variant report

Variant	rs10471774
Chromosome Location	chr5:68616331-68616332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAF9-3	chr5:68616292-68616410	NONHSAT101908
2	lnc-TAF9-3	chr5:68616064-68616407	NONHSAT101909

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10035835	0.85[AFR][1000 genomes]
rs10038816	0.85[AFR][1000 genomes]
rs10044508	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10045526	0.90[ASN][1000 genomes]
rs10064264	0.85[AFR][1000 genomes]
rs10068576	0.85[AFR][1000 genomes]
rs10077458	0.85[AFR][1000 genomes]
rs10078100	0.85[AFR][1000 genomes]
rs10471350	0.80[EUR][1000 genomes]
rs10471775	0.80[EUR][1000 genomes]
rs10940212	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10940214	0.85[EUR][1000 genomes]
rs10940216	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10940218	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1168409	0.85[AFR][1000 genomes]
rs11748974	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1177556	0.85[AFR][1000 genomes]
rs12187268	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12188076	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12513817	0.84[ASN][1000 genomes]
rs12517724	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13362324	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1530290	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2561172	0.85[AFR][1000 genomes]
rs2561186	0.85[AFR][1000 genomes]
rs28580747	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs299088	0.85[AFR][1000 genomes]
rs299091	0.85[AFR][1000 genomes]
rs299098	0.85[AFR][1000 genomes]
rs299099	0.85[AFR][1000 genomes]
rs299102	0.85[AFR][1000 genomes]
rs34935424	0.85[EUR][1000 genomes]
rs350104	0.86[CHB][hapmap]
rs3890705	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4252228	0.90[AFR][1000 genomes]
rs4266362	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4473723	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4976160	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4976189	0.85[EUR][1000 genomes]
rs4976190	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4976194	0.81[EUR][1000 genomes]
rs58772585	0.82[EUR][1000 genomes]
rs60299793	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62373181	0.84[ASN][1000 genomes]
rs62373187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6450026	0.81[ASN][1000 genomes]
rs6450029	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6450032	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs676012	0.86[CHB][hapmap]
rs6866993	0.82[AMR][1000 genomes]
rs6873869	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6875069	0.81[EUR][1000 genomes]
rs6879078	0.80[EUR][1000 genomes]
rs7708429	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7712318	0.96[AFR][1000 genomes]
rs9291947	0.80[EUR][1000 genomes]
rs9291948	0.80[EUR][1000 genomes]
rs9791036	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv969960	chr5:68613678-68646127	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10471774	MRPS36	cis	lymphoblastoid	seeQTL
rs10471774	CCDC125	cis	lung	GTEx
rs10471774	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs10471774	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
2	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
4	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
6	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
7	chr5:68577600-68619800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:68577600-68627400	Weak transcription	NHEK	skin
9	chr5:68577800-68626600	Weak transcription	A549	lung
10	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:68581800-68617800	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:68581800-68626800	Weak transcription	Fetal Brain Female	brain
13	chr5:68581800-68627600	Weak transcription	Brain Anterior Caudate	brain
14	chr5:68582800-68622400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:68591600-68627600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:68596000-68626800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr5:68599600-68627800	Weak transcription	NH-A	brain
18	chr5:68601400-68627600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:68605600-68627400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:68606200-68625600	Weak transcription	Hela-S3	cervix
21	chr5:68609400-68622400	Weak transcription	K562	blood
22	chr5:68609600-68624000	Weak transcription	Placenta	Placenta
23	chr5:68609600-68627400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr5:68609600-68627600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:68609800-68617600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:68609800-68621000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:68609800-68621000	Weak transcription	Thymus	Thymus
28	chr5:68609800-68627200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:68609800-68627400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:68609800-68627400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:68609800-68627400	Weak transcription	Esophagus	oesophagus
32	chr5:68609800-68627400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:68609800-68627400	Weak transcription	GM12878-XiMat	blood
34	chr5:68609800-68627600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr5:68609800-68627600	Weak transcription	Fetal Thymus	thymus
36	chr5:68609800-68628200	Weak transcription	Right Ventricle	heart
37	chr5:68609800-68628400	Weak transcription	Lung	lung
38	chr5:68610000-68619600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:68610000-68620200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:68610000-68621200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:68610000-68623600	Weak transcription	Fetal Intestine Large	intestine
42	chr5:68610000-68627400	Weak transcription	Dnd41	blood
43	chr5:68610400-68627600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr5:68610600-68621600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:68610600-68627800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:68611000-68628200	Weak transcription	Aorta	Aorta
47	chr5:68612400-68627400	Weak transcription	Adipose Nuclei	Adipose
48	chr5:68612600-68616800	Weak transcription	HepG2	liver
49	chr5:68612600-68618600	Weak transcription	Ovary	ovary
50	chr5:68612800-68626600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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