Variant report

Variant	rs6561551
Chromosome Location	chr13:50258449-50258450
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	chr13:50258208..50260676-chr13:50262902..50265227,2	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];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs1535544	0.89[ASW][hapmap];0.81[CEU][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.83[MKK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs1570407	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1885539	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2407797	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3903768	0.86[JPT][hapmap]
rs61959934	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61959936	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7319110	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7325692	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7327024	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs737250	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];0.99[ASN][1000 genomes]
rs737251	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316473	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs942030	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs942031	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];0.99[ASN][1000 genomes]
rs9526590	0.85[EUR][1000 genomes]
rs9535292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535296	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535297	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535299	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568303	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568304	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]
rs9568305	0.92[AMR][1000 genomes];1.00[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
rs6561551	TRIM13	cis	cerebellum	SCAN
rs6561551	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs6561551	KCNRG	cis	cerebellum	SCAN
rs6561551	RCBTB1	cis	cerebellum	SCAN
rs6561551	HTR2A	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50235600-50259800	Weak transcription	Right Ventricle	heart
2	chr13:50241000-50264800	Weak transcription	Aorta	Aorta
3	chr13:50242200-50260600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr13:50242200-50261000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr13:50242200-50261400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr13:50242200-50264200	Weak transcription	K562	blood
7	chr13:50242200-50264400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr13:50242200-50264400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr13:50242400-50260200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr13:50242400-50260400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr13:50242400-50261400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:50242400-50261400	Weak transcription	Gastric	stomach
13	chr13:50242400-50262200	Weak transcription	Spleen	Spleen
14	chr13:50242400-50263200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr13:50242400-50263800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr13:50242400-50264000	Weak transcription	Thymus	Thymus
17	chr13:50242400-50264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:50242400-50264400	Weak transcription	Adipose Nuclei	Adipose
19	chr13:50242400-50264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr13:50242600-50260000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr13:50244400-50264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr13:50245800-50261400	Weak transcription	HUVEC	blood vessel
23	chr13:50246000-50264600	Weak transcription	Left Ventricle	heart
24	chr13:50246200-50261400	Weak transcription	Hela-S3	cervix
25	chr13:50247000-50264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr13:50248400-50263600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr13:50249400-50263600	Weak transcription	Primary B cells from cord blood	blood
28	chr13:50250200-50260000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr13:50250400-50264400	Weak transcription	Primary T cells from cord blood	blood
30	chr13:50251400-50264400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr13:50251600-50264400	Weak transcription	HSMMtube	muscle
32	chr13:50251800-50262200	Weak transcription	Pancreas	Pancrea
33	chr13:50251800-50263600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr13:50252000-50259400	Weak transcription	Liver	Liver
35	chr13:50252600-50259600	Weak transcription	Lung	lung
36	chr13:50253200-50259600	Weak transcription	Fetal Intestine Large	intestine
37	chr13:50253600-50258600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr13:50253600-50264800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr13:50253800-50260000	Weak transcription	HepG2	liver
40	chr13:50253800-50261400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr13:50253800-50264000	Weak transcription	Ovary	ovary
42	chr13:50253800-50264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr13:50253800-50264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr13:50254000-50260200	Weak transcription	Fetal Thymus	thymus
45	chr13:50254000-50264400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:50254200-50259400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr13:50254200-50259600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr13:50254400-50258600	Weak transcription	Fetal Intestine Small	intestine
49	chr13:50254400-50259600	Weak transcription	Fetal Stomach	stomach
50	chr13:50254400-50260000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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