Variant report

Variant	rs7990502
Chromosome Location	chr13:50577868-50577869
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50571846..50573402-chr13:50576852..50578789,2	MCF-7	breast:
2	chr13:50576641..50578970-chr13:50694354..50696520,2	K562	blood:
3	chr13:50577257..50579543-chr13:50698927..50702304,3	K562	blood:

Variant related genes	Relation type
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1043208	0.83[EUR][1000 genomes]
rs10492746	0.83[EUR][1000 genomes]
rs1063181	0.85[EUR][1000 genomes]
rs1063183	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12100038	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12100048	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12583615	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs12583637	0.89[EUR][1000 genomes]
rs12583652	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12583823	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12584069	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12584122	0.92[EUR][1000 genomes]
rs12585753	0.83[EUR][1000 genomes]
rs12585966	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17073655	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];1.00[EUR][1000 genomes]
rs17073682	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17073724	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17073826	1.00[CHB][hapmap]
rs1807033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2066540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2066546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2066547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2066552	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2066553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2066555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2066559	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2066562	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2066565	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2177313	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2181267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2181268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2407881	0.89[EUR][1000 genomes]
rs2407882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41308548	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4614628	0.81[EUR][1000 genomes]
rs55638467	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55727821	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55869555	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs57230741	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59931782	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60574696	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs60583460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60828549	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60926548	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs61960398	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61960442	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61960445	0.84[EUR][1000 genomes]
rs61960446	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61960447	0.83[EUR][1000 genomes]
rs61960449	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61960450	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61960451	0.83[EUR][1000 genomes]
rs61960454	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61960455	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61960457	0.87[EUR][1000 genomes]
rs61961261	0.87[EUR][1000 genomes]
rs61961263	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61961294	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61961298	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61961299	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61961301	0.85[EUR][1000 genomes]
rs61961302	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61961303	0.83[EUR][1000 genomes]
rs61961306	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs61961324	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6561571	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]
rs6561572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6561575	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6561576	0.82[AMR][1000 genomes]
rs66559968	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs66756338	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7140070	0.86[AFR][1000 genomes]
rs7319351	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73196731	0.89[EUR][1000 genomes]
rs7325091	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs732729	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7328892	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7334063	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];1.00[EUR][1000 genomes]
rs7336477	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7336927	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7339181	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs74078717	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7981648	1.00[CHB][hapmap]
rs7982125	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7984332	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];0.99[EUR][1000 genomes]
rs7984907	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7986364	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7986432	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7991454	0.85[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7992903	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7994224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7995557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7997305	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7997402	0.87[EUR][1000 genomes]
rs7997638	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7998223	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7998391	0.89[EUR][1000 genomes]
rs9670083	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7990502	TRIM13	cis	Nerve Tibial	GTEx
rs7990502	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs7990502	DLEU1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50571800-50585200	Weak transcription	Gastric	stomach
2	chr13:50572000-50578400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:50572000-50578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:50572000-50585800	Weak transcription	Ovary	ovary
5	chr13:50572600-50578400	Weak transcription	Esophagus	oesophagus
6	chr13:50572600-50579200	Weak transcription	HSMMtube	muscle
7	chr13:50572600-50589600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:50572800-50578800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:50572800-50584400	Weak transcription	K562	blood
10	chr13:50573000-50594600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:50573400-50580400	Weak transcription	Small Intestine	intestine
12	chr13:50573600-50578000	Strong transcription	Placenta	Placenta
13	chr13:50573600-50578600	Weak transcription	Spleen	Spleen
14	chr13:50573600-50580000	Weak transcription	Colonic Mucosa	Colon
15	chr13:50573800-50578200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr13:50573800-50578400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr13:50573800-50578400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr13:50573800-50578400	Strong transcription	NH-A	brain
19	chr13:50573800-50581000	Strong transcription	Fetal Thymus	thymus
20	chr13:50573800-50585000	Weak transcription	Left Ventricle	heart
21	chr13:50573800-50585800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr13:50573800-50588600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr13:50573800-50589400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr13:50573800-50590200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:50574000-50580400	Strong transcription	Osteobl	bone
26	chr13:50574000-50584800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr13:50574000-50585000	Weak transcription	Aorta	Aorta
28	chr13:50574000-50585600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:50574000-50586000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr13:50574000-50599600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:50574200-50578200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr13:50574200-50578200	Weak transcription	Fetal Muscle Leg	muscle
33	chr13:50574200-50581200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr13:50574200-50589000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr13:50574200-50591000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr13:50574400-50578800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr13:50574600-50578400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:50574600-50580000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
39	chr13:50574600-50588800	Weak transcription	Stomach Mucosa	stomach
40	chr13:50574800-50578200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:50574800-50578400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr13:50574800-50578400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr13:50574800-50578600	Genic enhancers	Dnd41	blood
44	chr13:50574800-50579800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr13:50574800-50580400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr13:50574800-50580400	Weak transcription	Brain Substantia Nigra	brain
47	chr13:50574800-50580600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr13:50574800-50580800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr13:50574800-50580800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr13:50574800-50584400	Weak transcription	Fetal Heart	heart

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