Variant report

Variant	rs9993676
Chromosome Location	chr4:110530197-110530198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10004265	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10017233	0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs10027051	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500353	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511564	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149801	0.87[ASN][1000 genomes]
rs183192	0.82[AMR][1000 genomes]
rs197205	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197208	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs197210	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs197211	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];0.88[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.98[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]
rs197214	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197215	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs197217	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]
rs197227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197232	0.82[AMR][1000 genomes]
rs197234	0.82[AMR][1000 genomes]
rs6533437	0.80[EUR][1000 genomes]
rs6533439	0.80[EUR][1000 genomes]
rs6533440	0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs6533441	0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6810719	0.87[TSI][hapmap]
rs6810809	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6811858	0.89[TSI][hapmap]
rs6818852	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6827415	0.86[ASN][1000 genomes]
rs6832174	0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs6841003	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841563	0.92[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	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
4	esv3419480	chr4:110521397-110549622	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9993676	CASP6	cis	parietal	SCAN
rs9993676	CASP6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110510800-110530800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:110522600-110531000	Weak transcription	Ovary	ovary
3	chr4:110524600-110531200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr4:110524800-110531000	Weak transcription	Dnd41	blood
5	chr4:110525000-110530200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:110525000-110530800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:110525000-110530800	Weak transcription	Spleen	Spleen
8	chr4:110525200-110531000	Weak transcription	Thymus	Thymus
9	chr4:110529000-110533200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:110529200-110531000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr4:110529400-110530800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:110529400-110531000	Strong transcription	Primary T cells from cord blood	blood
13	chr4:110529400-110531000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:110529600-110530600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:110529600-110531000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:110529800-110531600	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr4:110530000-110530200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:110530000-110530200	ZNF genes & repeats	Primary B cells from cord blood	blood
19	chr4:110530000-110530400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:110530000-110530400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:110530000-110530800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr4:110530000-110531000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr4:110530000-110531000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:110530000-110531400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:110530000-110531600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:110530000-110531600	Enhancers	Placenta	Placenta
27	chr4:110530000-110532000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr4:110530000-110532600	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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