Variant report

Variant	rs737930
Chromosome Location	chr22:31459255-31459256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr22:31459236-31460688	HCT-116	colon:	n/a	chr22:31459570-31459580 chr22:31459573-31459583
2	MAX	chr22:31459171-31459472	K562	blood:	n/a	n/a
3	FOS	chr22:31458577-31459311	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:31450718..31452880-chr22:31457371..31459942,3	MCF-7	breast:
2	chr22:31363691..31369255-chr22:31456002..31460514,7	MCF-7	breast:
3	chr22:31457775..31462699-chr22:31474304..31478789,5	MCF-7	breast:
4	chr22:31364481..31367281-chr22:31457492..31460562,3	MCF-7	breast:
5	chr22:31363776..31366652-chr22:31458331..31460655,2	K562	blood:
6	chr22:31451720..31453462-chr22:31457824..31459739,2	MCF-7	breast:
7	chr22:31458274..31462644-chr22:31476246..31482425,10	K562	blood:
8	chr22:31455769..31462183-chr22:31475245..31482356,13	K562	blood:
9	chr22:31455775..31461842-chr22:31476267..31480955,13	MCF-7	breast:

No data

Variant related genes	Relation type
SMTN	TF binding region
ENSG00000253352	Chromatin interaction
ENSG00000273387	Chromatin interaction
ENSG00000133422	Chromatin interaction
ENSG00000183963	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1004243	0.87[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes]
rs11089487	0.82[AMR][1000 genomes]
rs11089488	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11703478	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11705137	0.84[MKK][hapmap];0.81[YRI][hapmap]
rs12167220	0.84[MKK][hapmap];0.81[YRI][hapmap]
rs12330010	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12484046	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13054770	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1558023	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2079429	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35657209	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35685997	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4281997	0.81[AMR][1000 genomes]
rs4820934	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820940	0.81[YRI][hapmap]
rs7284108	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7284757	0.91[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs7285617	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8135353	0.91[CEU][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9619163	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9621173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9621178	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9621184	0.96[CEU][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9621185	0.96[CEU][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9621187	0.83[AMR][1000 genomes]
rs9621188	0.84[MKK][hapmap];0.81[YRI][hapmap]

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	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv524366	chr22:31440703-31480069	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv964620	chr22:31452981-31465140	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv962852	chr22:31455516-31465140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs737930	CHEK2	cis	cerebellum	SCAN
rs737930	SELM	cis	parietal	SCAN
rs737930	CRYBB1	cis	cerebellum	SCAN
rs737930	CCDC117	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31456200-31460000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr22:31456200-31460000	Weak transcription	A549	lung
3	chr22:31456600-31461000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr22:31457000-31465400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr22:31457800-31459400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr22:31458200-31459400	Enhancers	NHEK	skin
7	chr22:31458200-31459600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr22:31458200-31459600	Enhancers	HMEC	breast
9	chr22:31458200-31459800	Enhancers	Fetal Intestine Large	intestine
10	chr22:31458400-31459800	Enhancers	Fetal Intestine Small	intestine
11	chr22:31458600-31459600	Weak transcription	Hela-S3	cervix
12	chr22:31458800-31465200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr22:31459200-31459600	Enhancers	HepG2	liver
14	chr22:31459200-31459800	Flanking Active TSS	K562	blood

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