Variant report

Variant	rs7339181
Chromosome Location	chr13:50641176-50641177
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50637584..50641226-chr13:50648962..50651293,3	K562	blood:
2	chr13:50640517..50642548-chr13:50652959..50655248,2	K562	blood:
3	chr13:50638410..50642177-chr13:50643409..50648630,6	K562	blood:
4	chr13:50640962..50642807-chr13:50646413..50649887,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLEU1-1	chr13:50639582-50641525	NONHSAT033807

Extended variants
information (count: 115 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1043208	1.00[ASN][1000 genomes]
rs10492746	1.00[ASN][1000 genomes]
rs1063181	0.84[ASN][1000 genomes]
rs1063183	0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs12100038	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12100048	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583615	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs12583637	1.00[ASN][1000 genomes]
rs12583652	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12583823	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12584069	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12585753	1.00[ASN][1000 genomes]
rs12585966	0.85[AFR][1000 genomes]
rs1323451	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073655	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17073682	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17073724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073826	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1807033	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2066540	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2066546	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2066547	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2066552	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2066553	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2066555	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2066559	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066562	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066565	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066566	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066586	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2066598	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs2177313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181267	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.84[ASN][1000 genomes]
rs2181268	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2407881	0.95[ASN][1000 genomes]
rs2407882	0.94[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs41308548	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs55638467	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs55727821	0.84[ASN][1000 genomes]
rs55869555	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs57230741	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs59931782	0.95[ASN][1000 genomes]
rs60574696	0.86[AFR][1000 genomes]
rs60583460	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60828549	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60926548	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960398	0.82[AFR][1000 genomes]
rs61960442	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61960445	0.84[ASN][1000 genomes]
rs61960446	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61960449	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61960450	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61960451	0.84[ASN][1000 genomes]
rs61960454	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61960455	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61960457	0.95[ASN][1000 genomes]
rs61961261	0.95[ASN][1000 genomes]
rs61961263	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61961294	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61961298	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61961299	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61961301	1.00[ASN][1000 genomes]
rs61961302	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61961303	1.00[ASN][1000 genomes]
rs61961304	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961305	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961306	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961323	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961324	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961325	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961327	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961328	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561571	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6561572	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6561575	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561576	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66559968	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66756338	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7140070	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7319351	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73196708	0.84[ASN][1000 genomes]
rs73196731	1.00[ASN][1000 genomes]
rs73196734	1.00[ASN][1000 genomes]
rs73196744	0.95[ASN][1000 genomes]
rs7325091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs7325993	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs732729	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs7328892	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7334063	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7336477	0.95[ASN][1000 genomes]
rs7336927	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74078717	0.83[AFR][1000 genomes]
rs790944	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981648	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap]
rs7982125	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs7984332	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7984907	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7986364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7986432	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7990502	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7991454	0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs7992903	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7994224	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7995557	0.94[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7997305	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7997402	0.95[ASN][1000 genomes]
rs7997638	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7998223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998391	1.00[ASN][1000 genomes]
rs9670083	0.82[AFR][1000 genomes];0.84[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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv1054415	chr13:50598121-50650938	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1202 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7339181	C13orf1	cis	cerebellum	SCAN
rs7339181	TRIM13	cis	cerebellum	SCAN
rs7339181	PCDH8	cis	parietal	SCAN
rs7339181	RB1	cis	cerebellum	SCAN
rs7339181	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs7339181	DLEU1	cis	lymphoblastoid	seeQTL
rs7339181	KIAA1704	cis	cerebellum	SCAN
rs7339181	DLEU1	Cis_1M	lymphoblastoid	RTeQTL
rs7339181	KCNRG	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50578800-50654400	Weak transcription	Esophagus	oesophagus
2	chr13:50586800-50654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:50587000-50645600	Weak transcription	Spleen	Spleen
4	chr13:50588000-50645600	Weak transcription	Ovary	ovary
5	chr13:50589800-50645600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr13:50590200-50653600	Weak transcription	Small Intestine	intestine
7	chr13:50594800-50643200	Weak transcription	Brain Hippocampus Middle	brain
8	chr13:50594800-50643600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr13:50595000-50654200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr13:50595800-50654400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:50598600-50650200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr13:50611800-50646400	Strong transcription	Fetal Thymus	thymus
13	chr13:50612400-50643000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr13:50612600-50644200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:50612800-50645400	Weak transcription	HSMMtube	muscle
16	chr13:50614000-50643800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr13:50615200-50643200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr13:50616000-50653600	Weak transcription	Fetal Kidney	kidney
19	chr13:50617400-50650000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr13:50617400-50654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:50621400-50645600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr13:50622600-50653400	Weak transcription	Fetal Brain Male	brain
23	chr13:50622800-50653400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr13:50623400-50645600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr13:50624400-50654200	Weak transcription	Pancreas	Pancrea
26	chr13:50625400-50654200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:50625600-50649000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr13:50626600-50654000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr13:50628400-50652400	Weak transcription	Psoas Muscle	Psoas
30	chr13:50630000-50651000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr13:50630600-50645600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr13:50630800-50645400	Weak transcription	Brain Anterior Caudate	brain
33	chr13:50631200-50645200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr13:50631200-50646200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr13:50631800-50645400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr13:50633000-50653600	Weak transcription	Fetal Stomach	stomach
37	chr13:50633400-50642400	Weak transcription	Gastric	stomach
38	chr13:50633400-50652200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr13:50634600-50642800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr13:50634800-50642800	Weak transcription	Brain Substantia Nigra	brain
41	chr13:50634800-50644000	Weak transcription	Aorta	Aorta
42	chr13:50635000-50643400	Weak transcription	A549	lung
43	chr13:50635000-50645000	Weak transcription	Brain Germinal Matrix	brain
44	chr13:50635200-50643400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr13:50636000-50642400	Strong transcription	Osteobl	bone
46	chr13:50636800-50643600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr13:50637000-50645600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr13:50637200-50642600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr13:50637200-50642600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:50637200-50643200	Strong transcription	HSMM	muscle

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