Variant report

Variant	rs667923
Chromosome Location	chr1:84871977-84871978
allele	A/G
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	MAX	chr1:84871801-84872720	HCT-116	colon:	n/a	n/a
2	SP1	chr1:84871957-84872818	HCT-116	colon:	n/a	n/a
3	NFIC	chr1:84871942-84872711	SK-N-SH	brain:	n/a	n/a
4	FOSL1	chr1:84871977-84872760	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
DNASE2B	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10493747	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10874438	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11163962	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049602	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12118984	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12406723	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1246330	0.95[EUR][1000 genomes]
rs1246331	0.93[EUR][1000 genomes]
rs1588037	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17131704	0.93[ASN][1000 genomes]
rs500565	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs558268	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs646681	0.88[GIH][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs6576704	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6661172	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs679152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511984	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7512262	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7514601	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7515964	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7516125	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541465	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7547088	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7548231	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9432829	0.93[ASN][1000 genomes]
rs9433225	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs667923	HS2ST1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84868000-84872200	Weak transcription	HUVEC	blood vessel
2	chr1:84868000-84872200	Weak transcription	NHDF-Ad	bronchial
3	chr1:84868600-84872000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:84868600-84872000	Weak transcription	NHEK	skin
5	chr1:84869000-84872200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:84869600-84873600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:84869800-84873400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:84870200-84874200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr1:84871000-84874400	Enhancers	Fetal Intestine Large	intestine
10	chr1:84871200-84874200	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:84871200-84874400	Enhancers	Fetal Intestine Small	intestine
12	chr1:84871400-84873600	Weak transcription	Colonic Mucosa	Colon
13	chr1:84871800-84872000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:84871800-84873000	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links