Variant report

Variant	rs9535341
Chromosome Location	chr13:50363304-50363305
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	chr13:50266035..50267824-chr13:50362193..50365135,2	K562	blood:
2	chr13:50363119..50364738-chr13:50365543..50368287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1009333	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10492591	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1127021	0.95[YRI][hapmap]
rs1198315	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1198319	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1198320	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1198322	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1198324	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1198327	0.84[EUR][1000 genomes]
rs1198328	0.82[EUR][1000 genomes]
rs1201716	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1211304	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1407440	0.88[ASW][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs1407441	0.88[ASW][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs1547623	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1570353	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1581745	0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2146143	0.87[GIH][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap]
rs2181185	0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2407804	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2897770	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3851162	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3851164	0.83[EUR][1000 genomes]
rs3851166	0.81[EUR][1000 genomes]
rs4942863	0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4942866	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55732704	0.81[EUR][1000 genomes]
rs59641461	0.81[EUR][1000 genomes]
rs61961491	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61961500	0.84[EUR][1000 genomes]
rs61961501	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs61961502	0.84[EUR][1000 genomes]
rs6561552	0.87[GIH][hapmap];0.81[YRI][hapmap]
rs6561560	1.00[GIH][hapmap]
rs73194445	0.84[EUR][1000 genomes]
rs7330392	0.86[AMR][1000 genomes]
rs7983303	0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7984061	0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7996307	0.81[EUR][1000 genomes]
rs9316474	0.88[ASW][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9316476	0.81[EUR][1000 genomes]
rs9526593	0.95[YRI][hapmap]
rs9535305	0.95[YRI][hapmap]
rs9535307	0.94[YRI][hapmap]
rs9535310	0.88[ASW][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs9535316	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9535340	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9562927	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9596197	0.83[EUR][1000 genomes]
rs9596200	0.81[EUR][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	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv900074	chr13:50317104-50381016	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv900075	chr13:50331992-50376858	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9535341	EBPL	cis	cerebellum	SCAN
rs9535341	KCNRG	cis	cerebellum	SCAN
rs9535341	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs9535341	TRIM13	cis	cerebellum	SCAN
rs9535341	RCBTB1	cis	cerebellum	SCAN
rs9535341	HTR2A	cis	parietal	SCAN
rs9535341	STK32C	trans	cerebellum	SCAN
rs9535341	RB1	cis	cerebellum	SCAN
rs9535341	SNORA31	cis	cerebellum	SCAN
rs9535341	SIAH3	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr13:50336200-50364800	Weak transcription	Fetal Intestine Small	intestine
3	chr13:50336800-50364600	Weak transcription	NHLF	lung
4	chr13:50349600-50365400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:50349600-50365400	Weak transcription	Lung	lung
6	chr13:50351200-50364200	Weak transcription	HSMM	muscle
7	chr13:50351200-50364600	Weak transcription	HSMMtube	muscle
8	chr13:50351600-50363800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr13:50351800-50363800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:50351800-50364000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr13:50352000-50365200	Weak transcription	Fetal Thymus	thymus
12	chr13:50352400-50364400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr13:50352600-50363800	Weak transcription	Pancreas	Pancrea
14	chr13:50352600-50363800	Weak transcription	Thymus	Thymus
15	chr13:50352600-50364800	Weak transcription	A549	lung
16	chr13:50353000-50363800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr13:50353000-50363800	Weak transcription	Small Intestine	intestine
18	chr13:50353800-50363800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr13:50354200-50363800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr13:50354200-50363800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr13:50354200-50364400	Weak transcription	Right Atrium	heart
22	chr13:50354200-50365400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr13:50354400-50363600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr13:50354400-50365400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr13:50356200-50363800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr13:50356200-50364800	Weak transcription	NHEK	skin
27	chr13:50356400-50364000	Weak transcription	Brain Anterior Caudate	brain
28	chr13:50356400-50365200	Weak transcription	Right Ventricle	heart
29	chr13:50356600-50365000	Weak transcription	Fetal Kidney	kidney
30	chr13:50356800-50364600	Weak transcription	Primary B cells from cord blood	blood
31	chr13:50357000-50363600	Weak transcription	Fetal Brain Female	brain
32	chr13:50357000-50364400	Weak transcription	Ovary	ovary
33	chr13:50357800-50364000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr13:50357800-50364200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr13:50357800-50364600	Weak transcription	Fetal Stomach	stomach
36	chr13:50357800-50365200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr13:50358400-50363800	Weak transcription	Left Ventricle	heart
38	chr13:50358400-50364400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr13:50358400-50364600	Weak transcription	Aorta	Aorta
40	chr13:50358400-50365200	Weak transcription	Stomach Mucosa	stomach
41	chr13:50358400-50365600	Weak transcription	Gastric	stomach
42	chr13:50359200-50363800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr13:50359600-50363600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr13:50359600-50364000	Weak transcription	Adipose Nuclei	Adipose
45	chr13:50359600-50365200	Weak transcription	Fetal Muscle Leg	muscle
46	chr13:50359800-50363800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr13:50359800-50364000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr13:50360000-50363600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr13:50360000-50363800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr13:50360000-50364000	Weak transcription	Osteobl	bone

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