Variant report

Variant	rs197217
Chromosome Location	chr4:110521328-110521329
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10004265	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017233	0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs10027051	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500353	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511564	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149801	0.87[ASN][1000 genomes]
rs183192	0.80[AMR][1000 genomes]
rs197205	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197208	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs197210	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs197211	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197212	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197215	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs197227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197232	0.80[AMR][1000 genomes]
rs197234	0.80[AMR][1000 genomes]
rs6533437	0.81[EUR][1000 genomes]
rs6533439	0.81[EUR][1000 genomes]
rs6533440	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs6533441	0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6810719	0.87[TSI][hapmap]
rs6810809	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811858	0.89[TSI][hapmap]
rs6818852	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6827415	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6832174	0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs6841003	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841563	0.93[EUR][1000 genomes]
rs9993676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs197217	CASP6	cis	cerebellum	SCAN
rs197217	CASP6	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110508800-110523200	Weak transcription	Primary B cells from cord blood	blood
2	chr4:110510600-110522800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:110510800-110524200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:110510800-110530800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:110511000-110521600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:110511000-110527200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:110511400-110524400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:110512400-110530000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:110512800-110524000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr4:110512800-110524200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:110519800-110521800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr4:110519800-110521800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr4:110519800-110522000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr4:110519800-110524400	Weak transcription	Thymus	Thymus
15	chr4:110520000-110521800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:110520200-110521800	Enhancers	Primary T cells from cord blood	blood
17	chr4:110520200-110521800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr4:110520400-110522600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:110520600-110521800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr4:110521000-110521600	Weak transcription	Fetal Thymus	thymus
21	chr4:110521000-110521800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr4:110521200-110521800	ZNF genes & repeats	Dnd41	blood
23	chr4:110521200-110524200	Weak transcription	Primary T cells fromperipheralblood	blood

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