Variant report

Variant	rs9568304
Chromosome Location	chr13:50255751-50255752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50254223..50257561-chr13:50258855..50261948,4	K562	blood:
2	chr13:50252667..50256255-chr13:50260389..50264756,4	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13313256	0.85[JPT][hapmap]
rs1535470	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs1535544	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs1570407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2407797	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3903768	0.86[JPT][hapmap]
rs61959934	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61959936	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6561551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7319110	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7325692	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7327024	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs737250	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs737251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316473	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs942030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs942031	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.99[ASN][1000 genomes]
rs9526590	0.84[EUR][1000 genomes]
rs9535292	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535296	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535299	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591296	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9568304	TRIM13	cis	cerebellum	SCAN
rs9568304	RCBTB1	cis	cerebellum	SCAN
rs9568304	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs9568304	HTR2A	cis	parietal	SCAN
rs9568304	KCNRG	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50231800-50256000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr13:50235600-50259800	Weak transcription	Right Ventricle	heart
3	chr13:50237000-50256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr13:50237400-50256000	Weak transcription	NH-A	brain
5	chr13:50241000-50264800	Weak transcription	Aorta	Aorta
6	chr13:50241800-50256000	Weak transcription	HMEC	breast
7	chr13:50242200-50256200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr13:50242200-50260600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr13:50242200-50261000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr13:50242200-50261400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr13:50242200-50264200	Weak transcription	K562	blood
12	chr13:50242200-50264400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr13:50242200-50264400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr13:50242400-50256200	Weak transcription	Brain Substantia Nigra	brain
15	chr13:50242400-50260200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr13:50242400-50260400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr13:50242400-50261400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr13:50242400-50261400	Weak transcription	Gastric	stomach
19	chr13:50242400-50262200	Weak transcription	Spleen	Spleen
20	chr13:50242400-50263200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr13:50242400-50263800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr13:50242400-50264000	Weak transcription	Thymus	Thymus
23	chr13:50242400-50264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr13:50242400-50264400	Weak transcription	Adipose Nuclei	Adipose
25	chr13:50242400-50264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr13:50242600-50260000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr13:50244200-50256200	Weak transcription	Fetal Kidney	kidney
28	chr13:50244400-50264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr13:50244600-50255800	Weak transcription	NHDF-Ad	bronchial
30	chr13:50245600-50256000	Weak transcription	Osteobl	bone
31	chr13:50245600-50256200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr13:50245800-50255800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:50245800-50256400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:50245800-50261400	Weak transcription	HUVEC	blood vessel
35	chr13:50246000-50264600	Weak transcription	Left Ventricle	heart
36	chr13:50246200-50261400	Weak transcription	Hela-S3	cervix
37	chr13:50247000-50264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr13:50247200-50256000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr13:50248400-50263600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr13:50249400-50263600	Weak transcription	Primary B cells from cord blood	blood
41	chr13:50249800-50255800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr13:50249800-50256000	Weak transcription	NHLF	lung
43	chr13:50250200-50260000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr13:50250400-50256000	Weak transcription	GM12878-XiMat	blood
45	chr13:50250400-50264400	Weak transcription	Primary T cells from cord blood	blood
46	chr13:50251400-50256000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr13:50251400-50264400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr13:50251600-50256200	Weak transcription	Fetal Lung	lung
49	chr13:50251600-50264400	Weak transcription	HSMMtube	muscle
50	chr13:50251800-50262200	Weak transcription	Pancreas	Pancrea

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