Variant report

Variant	rs6561571
Chromosome Location	chr13:50547126-50547127
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	chr13:50546165..50548667-chr13:50566546..50568183,2	MCF-7	breast:
2	chr13:50546094..50549679-chr13:50569848..50571713,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204977	Chromatin interaction
ENSG00000264864	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1043208	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10492746	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1063181	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1063183	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12100038	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12100048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12583615	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583637	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583652	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12583823	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12584069	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12584122	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12585753	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12585966	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1323451	0.95[ASN][1000 genomes]
rs17073655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17073682	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17073724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17073826	1.00[CHB][hapmap]
rs1807033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066546	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066547	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066552	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2066555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066559	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2066562	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2066565	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2066566	0.95[ASN][1000 genomes]
rs2177313	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2181267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2181268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2407881	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308548	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4614628	0.81[EUR][1000 genomes]
rs55638467	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55727821	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55869555	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57230741	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59931782	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60574696	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60583460	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60828549	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60926548	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61960398	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61960442	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960445	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960446	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960447	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61960449	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960450	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960451	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61960454	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960455	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61960457	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961261	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961294	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961298	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961299	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961301	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961302	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961303	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961304	0.95[ASN][1000 genomes]
rs61961305	0.95[ASN][1000 genomes]
rs61961306	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs61961323	0.95[ASN][1000 genomes]
rs61961324	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs61961325	0.95[ASN][1000 genomes]
rs61961327	0.95[ASN][1000 genomes]
rs61961328	0.95[ASN][1000 genomes]
rs6561572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6561576	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs66559968	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs66756338	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7140070	0.86[AFR][1000 genomes]
rs7319351	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73194486	0.84[ASN][1000 genomes]
rs73196708	0.89[ASN][1000 genomes]
rs73196731	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73196734	0.95[ASN][1000 genomes]
rs73196744	0.89[ASN][1000 genomes]
rs7325091	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs7325993	0.81[ASN][1000 genomes]
rs732729	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7328892	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7334063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336477	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336927	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7339181	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]
rs74078717	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs790944	0.95[ASN][1000 genomes]
rs7981648	1.00[CHB][hapmap]
rs7982125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7984332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7984907	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7986364	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7986432	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7991454	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7992903	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7997305	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997402	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997638	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7998223	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7998391	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9670083	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6561571	TRIM13	cis	Nerve Tibial	GTEx
rs6561571	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs6561571	DLEU1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50522400-50550600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:50529600-50550000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr13:50531400-50550400	Weak transcription	NHDF-Ad	bronchial
4	chr13:50533000-50552200	Weak transcription	Ovary	ovary
5	chr13:50534400-50550400	Weak transcription	HSMM	muscle
6	chr13:50535600-50547400	Weak transcription	Thymus	Thymus
7	chr13:50536400-50552800	Weak transcription	Fetal Heart	heart
8	chr13:50538200-50550400	Weak transcription	Brain Substantia Nigra	brain
9	chr13:50538200-50558000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr13:50538800-50550400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr13:50539000-50548800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr13:50539000-50570000	Weak transcription	Fetal Intestine Small	intestine
13	chr13:50539800-50550400	Weak transcription	A549	lung
14	chr13:50540000-50550400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:50540200-50562200	Weak transcription	Adipose Nuclei	Adipose
16	chr13:50540400-50547200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr13:50540400-50550400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:50540400-50550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:50540400-50569800	Weak transcription	Primary T cells from cord blood	blood
20	chr13:50540600-50549400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:50542600-50550800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr13:50543400-50547600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr13:50543600-50570400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:50544000-50549200	Weak transcription	Osteobl	bone
25	chr13:50545400-50555800	Weak transcription	Fetal Muscle Leg	muscle
26	chr13:50545400-50559000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr13:50545600-50547400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr13:50545800-50558000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:50545800-50562000	Weak transcription	Fetal Intestine Large	intestine
30	chr13:50546000-50569200	Weak transcription	Primary B cells from cord blood	blood
31	chr13:50546000-50570000	Weak transcription	NHLF	lung
32	chr13:50546200-50547800	Enhancers	Stomach Mucosa	stomach
33	chr13:50546600-50547800	Enhancers	HepG2	liver
34	chr13:50546600-50549600	Strong transcription	Fetal Thymus	thymus
35	chr13:50546800-50547200	Flanking Active TSS	Liver	Liver
36	chr13:50546800-50547200	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr13:50546800-50547200	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr13:50546800-50547200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr13:50546800-50550400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr13:50547000-50547600	Enhancers	Pancreas	Pancrea
41	chr13:50547000-50547600	Enhancers	Dnd41	blood
42	chr13:50547000-50550400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr13:50547000-50550800	Strong transcription	Skeletal Muscle Female	skeletal muscle

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