Variant report

Variant	rs9625933
Chromosome Location	chr22:30555216-30555217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30552521..30555409-chr22:30604715..30606658,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10048885	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11090598	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12167333	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12168499	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12171061	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12171250	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12171263	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17648725	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs193473	0.83[EUR][1000 genomes]
rs193481	0.84[EUR][1000 genomes]
rs1978083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412960	0.95[CEU][hapmap]
rs2412963	0.95[CEU][hapmap]
rs28257	0.82[EUR][1000 genomes]
rs3788423	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs41162	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs41164	0.95[CEU][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap]
rs41172	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap]
rs41174	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs41175	0.83[EUR][1000 genomes]
rs41177	0.80[CEU][hapmap]
rs41179	0.83[EUR][1000 genomes]
rs4239932	0.84[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs4239933	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4337577	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4823070	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62226440	0.86[AFR][1000 genomes]
rs718772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs737909	0.95[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs737912	0.95[CEU][hapmap]
rs7510705	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8135823	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8138286	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8141404	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8141765	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9614162	0.92[MKK][hapmap];0.82[YRI][hapmap]
rs9620943	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9620953	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625919	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625921	0.80[CEU][hapmap]
rs9625926	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9625931	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9625935	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv527188	chr22:30529741-30581722	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9625933	CRYBB3	cis	parietal	SCAN
rs9625933	TTC28	cis	cerebellum	SCAN
rs9625933	KIAA1671	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30547200-30555400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr22:30547200-30555600	Weak transcription	Thymus	Thymus
3	chr22:30550200-30555800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr22:30551600-30555600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr22:30553200-30555400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr22:30553800-30558200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr22:30554600-30556400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr22:30554600-30557200	Enhancers	Fetal Thymus	thymus
9	chr22:30554800-30557600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr22:30555000-30556000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr22:30555000-30556000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr22:30555000-30556400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr22:30555000-30557200	Enhancers	A549	lung
14	chr22:30555000-30557600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr22:30555200-30555400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr22:30555200-30555800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr22:30555200-30556200	Enhancers	NHLF	lung
18	chr22:30555200-30556400	Enhancers	Liver	Liver
19	chr22:30555200-30556400	Enhancers	Hela-S3	cervix
20	chr22:30555200-30556400	Enhancers	NH-A	brain
21	chr22:30555200-30556600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:30555200-30556600	Enhancers	Osteobl	bone
23	chr22:30555200-30557600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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