Variant report

Variant	rs3020825
Chromosome Location	chr4:55569146-55569147
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	chr4:55567098..55569303-chr4:55573075..55575854,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17240054	0.86[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2237019	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237020	0.81[EUR][1000 genomes]
rs2237021	0.82[EUR][1000 genomes]
rs2237023	1.00[ASW][hapmap];0.88[CEU][hapmap];0.98[GIH][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2282775	0.84[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2537866	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2537867	0.95[EUR][1000 genomes]
rs2703461	1.00[ASW][hapmap];0.88[CEU][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2703464	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2703488	0.81[GIH][hapmap];0.89[TSI][hapmap]
rs2855770	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2855777	0.81[GIH][hapmap];0.89[TSI][hapmap]
rs28729669	0.83[EUR][1000 genomes]
rs3020821	0.81[GIH][hapmap];0.89[TSI][hapmap]
rs3020826	0.82[EUR][1000 genomes]
rs3020827	0.84[CEU][hapmap];0.80[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3111800	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3134884	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs3134885	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864919	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6810872	0.87[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1003338	chr4:55566703-55582342	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3020825	SPINK2	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55545600-55575800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:55555200-55573600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:55555600-55574400	Weak transcription	Fetal Stomach	stomach
4	chr4:55557800-55594000	Weak transcription	Aorta	Aorta
5	chr4:55559600-55569600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:55561000-55606600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:55561200-55569200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:55561400-55572000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:55562000-55577200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:55562800-55597400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:55563200-55573400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:55564200-55569600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:55565000-55570200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:55565000-55573600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:55565000-55574000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:55565000-55576000	Weak transcription	Ovary	ovary
17	chr4:55565600-55575000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:55565600-55592800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr4:55566200-55569400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:55566200-55589600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:55566600-55569800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:55567000-55569800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:55567600-55575400	Weak transcription	Brain Germinal Matrix	brain
24	chr4:55567800-55574200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:55567800-55587200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:55568400-55569200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:55568600-55570800	Strong transcription	NHDF-Ad	bronchial
28	chr4:55568600-55571200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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