Variant report

Variant	rs61960446
Chromosome Location	chr13:50508971-50508972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50494914..50497363-chr13:50507125..50509301,2	MCF-7	breast:
2	chr13:50507293..50510312-chr13:50568081..50571220,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204977	Chromatin interaction
ENSG00000264864	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1043208	0.84[ASN][1000 genomes]
rs10492746	0.84[ASN][1000 genomes]
rs1063181	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1063183	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12100038	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100048	0.84[ASN][1000 genomes]
rs12583615	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12583637	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12583652	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12583823	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12584069	0.84[ASN][1000 genomes]
rs12584122	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12585753	0.84[ASN][1000 genomes]
rs12585966	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1323451	0.84[ASN][1000 genomes]
rs17073655	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17073682	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17073724	0.84[ASN][1000 genomes]
rs1807033	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066540	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066546	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066547	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066552	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066553	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2066555	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2066559	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2066562	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2066565	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2066566	0.84[ASN][1000 genomes]
rs2177313	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2181267	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181268	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407881	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2407882	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41308548	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614628	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55638467	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55727821	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55869555	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57230741	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59086590	0.81[EUR][1000 genomes]
rs59931782	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60574696	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60583460	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60828549	0.85[AFR][1000 genomes]
rs60926548	0.84[ASN][1000 genomes]
rs61960398	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61960442	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960445	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960447	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61960449	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960450	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960451	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960454	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960455	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960457	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61961261	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61961263	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61961294	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961298	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961299	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961301	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961302	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61961303	0.84[ASN][1000 genomes]
rs61961304	0.84[ASN][1000 genomes]
rs61961305	0.84[ASN][1000 genomes]
rs61961306	0.87[AFR][1000 genomes]
rs61961323	0.84[ASN][1000 genomes]
rs61961324	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs61961325	0.84[ASN][1000 genomes]
rs61961327	0.84[ASN][1000 genomes]
rs61961328	0.84[ASN][1000 genomes]
rs6561571	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6561572	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6561575	0.84[ASN][1000 genomes]
rs6561576	0.84[ASN][1000 genomes]
rs66559968	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs66756338	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7140070	0.81[AFR][1000 genomes]
rs7319351	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73194486	0.95[ASN][1000 genomes]
rs73196708	1.00[ASN][1000 genomes]
rs73196731	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73196734	0.84[ASN][1000 genomes]
rs732729	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328892	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334063	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7336477	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7336927	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7339181	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs74078717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs790944	0.84[ASN][1000 genomes]
rs7982125	0.84[ASN][1000 genomes]
rs7984332	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7984907	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7986364	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7986432	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7990502	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7991454	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7992903	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7994224	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7995557	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997305	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7997402	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7997638	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7998223	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7998391	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9670083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv976235	chr13:50501048-50509556	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs61960446	DLEU1	Cis_1M	lymphoblastoid	RTeQTL
rs61960446	TRIM13	cis	Nerve Tibial	GTEx
rs61960446	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50481800-50509600	Weak transcription	Right Ventricle	heart
2	chr13:50482600-50509600	Weak transcription	Primary B cells from cord blood	blood
3	chr13:50484000-50509600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:50484400-50509400	Weak transcription	Fetal Kidney	kidney
5	chr13:50484600-50509600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr13:50485800-50509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr13:50486000-50509400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr13:50486400-50509600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr13:50487400-50509400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr13:50487600-50509400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr13:50488400-50509600	Weak transcription	Colonic Mucosa	Colon
12	chr13:50489200-50509600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr13:50489200-50510000	Weak transcription	Spleen	Spleen
14	chr13:50492200-50509400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr13:50492400-50509600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr13:50492800-50509400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:50492800-50509600	Weak transcription	Aorta	Aorta
18	chr13:50493400-50509400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr13:50493800-50509600	Weak transcription	Lung	lung
20	chr13:50495400-50509600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr13:50497400-50509400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr13:50499000-50509400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr13:50499600-50509600	Weak transcription	Esophagus	oesophagus
24	chr13:50500000-50509400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr13:50500000-50509800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:50500600-50509200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr13:50502000-50509400	Weak transcription	HSMMtube	muscle
28	chr13:50502200-50509400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr13:50502600-50509600	Weak transcription	Pancreas	Pancrea
30	chr13:50502600-50509800	Weak transcription	Gastric	stomach
31	chr13:50502800-50509600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:50502800-50509600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr13:50502800-50509600	Weak transcription	Left Ventricle	heart
34	chr13:50503000-50509400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr13:50503000-50509400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr13:50503000-50509600	Weak transcription	HSMM	muscle
37	chr13:50503200-50509400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr13:50503200-50509600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr13:50503400-50509600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr13:50503400-50509600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr13:50503400-50509600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr13:50504000-50509600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr13:50504200-50509400	Weak transcription	Fetal Intestine Large	intestine
44	chr13:50504200-50509600	Weak transcription	Fetal Muscle Leg	muscle
45	chr13:50504200-50509600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr13:50504600-50509400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr13:50504800-50509400	Weak transcription	Fetal Stomach	stomach
48	chr13:50505800-50509000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr13:50505800-50509600	Weak transcription	Placenta	Placenta
50	chr13:50506400-50509400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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