Variant report

Variant	rs2053940
Chromosome Location	chr15:58860367-58860368
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	chr15:58858333..58860750-chr15:58870905..58872413,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10851638	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11635819	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11635859	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11636014	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11637823	1.00[AMR][1000 genomes]
rs12440615	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1978579	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2414602	1.00[AMR][1000 genomes]
rs2414603	1.00[AMR][1000 genomes]
rs2899633	1.00[AMR][1000 genomes]
rs35631005	1.00[AMR][1000 genomes]
rs4288939	1.00[AMR][1000 genomes]
rs4775080	1.00[AMR][1000 genomes]
rs4775081	1.00[AMR][1000 genomes]
rs4775082	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6494019	1.00[AMR][1000 genomes]
rs6494020	1.00[AMR][1000 genomes]
rs6494021	1.00[AMR][1000 genomes]
rs6494022	1.00[AMR][1000 genomes]
rs6494023	1.00[AMR][1000 genomes]
rs7163112	1.00[AMR][1000 genomes]
rs7164082	1.00[AMR][1000 genomes]
rs7168293	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7169280	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7176457	1.00[AMR][1000 genomes]
rs7180545	1.00[AMR][1000 genomes]
rs7180706	1.00[AMR][1000 genomes]
rs8038420	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv569601	chr15:58800766-58866156	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1050231	chr15:58848727-58863526	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1043560	chr15:58851369-58863526	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2053940	SOX30	trans	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58844600-58860400	Weak transcription	Primary T cells from cord blood	blood
2	chr15:58847200-58860400	Weak transcription	Thymus	Thymus
3	chr15:58852400-58860400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:58853200-58865000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:58854200-58860400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:58854200-58860400	Weak transcription	Pancreas	Pancrea
7	chr15:58854600-58860400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:58854600-58864200	Weak transcription	HepG2	liver
9	chr15:58854800-58868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:58857800-58860400	Weak transcription	Fetal Thymus	thymus
11	chr15:58857800-58860600	Weak transcription	Fetal Kidney	kidney
12	chr15:58857800-58862800	Weak transcription	Colonic Mucosa	Colon
13	chr15:58858400-58860400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:58858600-58860400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:58859000-58865600	Weak transcription	Liver	Liver
16	chr15:58859800-58861000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:58859800-58861200	Enhancers	K562	blood
18	chr15:58860200-58860600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr15:58860200-58860800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr15:58860200-58860800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr15:58860200-58860800	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr15:58860200-58860800	Enhancers	Stomach Mucosa	stomach
23	chr15:58860200-58860800	Enhancers	HMEC	breast
24	chr15:58860200-58861000	Enhancers	HUVEC	blood vessel
25	chr15:58860200-58861000	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr15:58860200-58861000	Enhancers	NHEK	skin
27	chr15:58860200-58861200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr15:58860200-58861200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr15:58860200-58861200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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