Variant report

Variant	rs9576280
Chromosome Location	chr13:38060247-38060248
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr13:38060210-38060706	HL-60	blood:	n/a	chr13:38060435-38060442 chr13:38060432-38060445
2	GATA3	chr13:38059676-38060349	SK-N-SH	brain:	n/a	chr13:38060336-38060343
3	PBX3	chr13:38059744-38060282	SK-N-SH	brain:	n/a	n/a
4	NFIC	chr13:38059740-38060371	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LINC01048	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12874878	0.97[ASN][1000 genomes]
rs1322809	0.83[ASN][1000 genomes]
rs1322810	0.82[ASN][1000 genomes]
rs17055871	0.84[ASW][hapmap]
rs2025246	0.83[ASN][1000 genomes]
rs2273894	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273895	0.85[ASN][1000 genomes]
rs4144252	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4144253	0.80[ASN][1000 genomes]
rs4144254	0.80[ASN][1000 genomes]
rs4144255	0.80[ASN][1000 genomes]
rs4391922	0.83[ASN][1000 genomes]
rs7319671	0.83[ASN][1000 genomes]
rs7323534	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7325567	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7326717	0.81[ASN][1000 genomes]
rs7329107	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7332389	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7983125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7984328	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7991077	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7995726	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7996210	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9532061	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9532063	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9547883	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9547900	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9566228	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9576271	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv899994	chr13:37816086-38087145	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1038850	chr13:37820489-38209571	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv34109	chr13:37843819-38276391	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv832582	chr13:37943056-38124252	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv832583	chr13:38030752-38202000	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9576280	STARD13	cis	cerebellum	SCAN
rs9576280	CRYL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38053600-38063600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:38055800-38065200	Weak transcription	HSMMtube	muscle
3	chr13:38056200-38065600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr13:38056400-38061600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr13:38058600-38065600	Weak transcription	Fetal Stomach	stomach
6	chr13:38059400-38064600	Enhancers	HSMM	muscle
7	chr13:38059400-38066000	Weak transcription	Colon Smooth Muscle	Colon
8	chr13:38059800-38060800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr13:38059800-38060800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:38059800-38060800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr13:38059800-38061200	Enhancers	NH-A	brain
12	chr13:38060000-38060400	Weak transcription	Fetal Lung	lung
13	chr13:38060000-38060800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr13:38060000-38060800	Flanking Active TSS	Osteobl	bone
15	chr13:38060000-38061400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:38060000-38061800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr13:38060200-38060600	Active TSS	Adipose Nuclei	Adipose
18	chr13:38060200-38060600	Active TSS	Right Atrium	heart
19	chr13:38060200-38060800	Active TSS	HUVEC	blood vessel
20	chr13:38060200-38060800	Active TSS	NHDF-Ad	bronchial
21	chr13:38060200-38060800	Active TSS	NHLF	lung
22	chr13:38060200-38065600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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