Variant report

Variant	rs11617754
Chromosome Location	chr13:50501980-50501981
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	chr13:50495816..50497958-chr13:50500274..50502867,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2066549	0.86[CHB][hapmap]
rs2066557	0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap]
rs2066571	0.81[ASN][1000 genomes]
rs2066575	0.86[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs2066585	0.86[CHB][hapmap]
rs2242482	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs2472599	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2475837	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2740524	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2740544	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs2740545	0.86[CHB][hapmap]
rs2760914	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs2803839	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs28798976	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3116591	0.85[ASN][1000 genomes]
rs4548769	0.86[CHB][hapmap]
rs4942899	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs7338055	0.82[ASN][1000 genomes]
rs73489861	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73489862	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs790943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs7986337	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535407	0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs9562941	0.82[CHB][hapmap]
rs9568348	0.81[CHB][hapmap]
rs9568354	0.81[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9568357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[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];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568359	0.82[CHB][hapmap]
rs9568363	0.80[ASN][1000 genomes]
rs9568364	0.80[ASN][1000 genomes]
rs9568366	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs9596219	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs9596220	0.86[CHB][hapmap];0.85[CHD][hapmap]

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	esv1851738	chr13:50474326-50507944	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv976235	chr13:50501048-50509556	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11617754	SCARNA1	trans	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50479600-50508600	Weak transcription	K562	blood
2	chr13:50480800-50508800	Weak transcription	Fetal Brain Male	brain
3	chr13:50481800-50509600	Weak transcription	Right Ventricle	heart
4	chr13:50482600-50509600	Weak transcription	Primary B cells from cord blood	blood
5	chr13:50484000-50509600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:50484400-50509400	Weak transcription	Fetal Kidney	kidney
7	chr13:50484600-50509600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr13:50485800-50506200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:50485800-50509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr13:50486000-50503400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr13:50486000-50503400	Strong transcription	Liver	Liver
12	chr13:50486000-50509400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr13:50486400-50509600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr13:50486600-50508800	Weak transcription	Hela-S3	cervix
15	chr13:50487400-50509400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr13:50487600-50509400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr13:50488400-50509600	Weak transcription	Colonic Mucosa	Colon
18	chr13:50489200-50509600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr13:50489200-50510000	Weak transcription	Spleen	Spleen
20	chr13:50489600-50502400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:50489600-50503200	Strong transcription	Adipose Nuclei	Adipose
22	chr13:50489600-50504200	Strong transcription	Fetal Intestine Large	intestine
23	chr13:50490200-50502800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr13:50490200-50503000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr13:50490800-50502000	Weak transcription	Primary T cells from cord blood	blood
26	chr13:50490800-50506200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr13:50491200-50507000	Weak transcription	Brain Angular Gyrus	brain
28	chr13:50492200-50504600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr13:50492200-50509400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr13:50492400-50509600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr13:50492600-50508800	Weak transcription	HUVEC	blood vessel
32	chr13:50492800-50509400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr13:50492800-50509600	Weak transcription	Aorta	Aorta
34	chr13:50493400-50502000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:50493400-50509400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr13:50493800-50509600	Weak transcription	Lung	lung
37	chr13:50494000-50502800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr13:50494200-50508800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr13:50494400-50508800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr13:50495400-50509600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr13:50495800-50508400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr13:50495800-50508800	Weak transcription	Brain Substantia Nigra	brain
43	chr13:50495800-50508800	Weak transcription	Fetal Brain Female	brain
44	chr13:50495800-50508800	Weak transcription	HepG2	liver
45	chr13:50496000-50506600	Weak transcription	NHLF	lung
46	chr13:50496000-50507000	Weak transcription	Psoas Muscle	Psoas
47	chr13:50497400-50503000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr13:50497400-50509400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr13:50497600-50502600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr13:50497600-50505400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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