Variant report

Variant	rs4820934
Chromosome Location	chr22:31456006-31456007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:31455777-31456050	K562	blood:	n/a	n/a
2	FOSL2	chr22:31455699-31456050	HepG2	liver:	n/a	n/a
3	MAFK	chr22:31455743-31456190	K562	blood:	n/a	chr22:31455875-31455884 chr22:31455870-31455885 chr22:31455875-31455885 chr22:31455874-31455888

No.	Distal block	Cell Line	Cell type
1	chr22:31363691..31369255-chr22:31456002..31460514,7	MCF-7	breast:
2	chr22:31363469..31366268-chr22:31450278..31456884,6	MCF-7	breast:
3	chr22:31455769..31462183-chr22:31475245..31482356,13	K562	blood:
4	chr22:31455775..31461842-chr22:31476267..31480955,13	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMTN-2	chr22:31455975-31456269	NONHSAT084842

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

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1004243	0.83[CEU][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes]
rs11089487	0.81[AMR][1000 genomes]
rs11089488	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11703478	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11705137	0.81[YRI][hapmap]
rs12167220	0.81[YRI][hapmap]
rs12330010	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12484046	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs13054770	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1558023	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2079429	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35657209	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35685997	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4281997	0.80[AMR][1000 genomes]
rs7284108	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7284757	0.87[CEU][hapmap]
rs7285617	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs737930	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]
rs8135353	0.88[CEU][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9619163	0.96[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9621173	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9621178	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9621184	0.91[CEU][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9621185	0.92[CEU][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9621187	0.82[AMR][1000 genomes]
rs9621188	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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31452000-31458000	Weak transcription	Adipose Nuclei	Adipose
2	chr22:31452800-31456800	Weak transcription	Hela-S3	cervix
3	chr22:31452800-31458200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr22:31455400-31456200	Enhancers	Fetal Lung	lung
5	chr22:31455400-31456200	Enhancers	Fetal Stomach	stomach
6	chr22:31455400-31458400	Enhancers	K562	blood
7	chr22:31455600-31456200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr22:31455600-31456200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr22:31455600-31456200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr22:31455600-31456200	Enhancers	A549	lung
11	chr22:31455600-31456400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:31455600-31456400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr22:31455600-31456400	Enhancers	Fetal Intestine Large	intestine
14	chr22:31455600-31456400	Enhancers	Fetal Intestine Small	intestine
15	chr22:31455600-31456400	Enhancers	Placenta	Placenta
16	chr22:31455600-31456400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr22:31455600-31456600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr22:31455600-31457000	Enhancers	HepG2	liver
19	chr22:31455600-31457600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr22:31455800-31456200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr22:31455800-31456200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr22:31455800-31456400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr22:31455800-31457400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr22:31455800-31458400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr22:31456000-31456200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr22:31456000-31456200	Enhancers	NHEK	skin
27	chr22:31456000-31458200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr22:31456000-31458200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr22:31456000-31458200	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links