Variant report

Variant	rs7954006
Chromosome Location	chr12:123131824-123131825
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123130027..123132200-chr12:123236586..123238656,2	K562	blood:
2	chr12:123130027..123133607-chr12:123236586..123238656,5	K562	blood:

Variant related genes	Relation type
ENSG00000139726	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10734924	0.89[ASW][hapmap];0.86[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs10744275	0.95[ASN][1000 genomes]
rs10744287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10773208	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs10773302	0.93[ASN][1000 genomes]
rs10773394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10846921	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10846978	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap]
rs10847179	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap];0.93[ASN][1000 genomes]
rs10847242	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10847415	0.95[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10998	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap]
rs11058226	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11058402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1392236	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1473553	0.89[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap]
rs1973463	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2062506	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2173628	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3803005	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4319547	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6489071	0.87[ASN][1000 genomes]
rs6489156	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs6489157	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6489158	0.95[ASN][1000 genomes]
rs7295105	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295397	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7307233	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307735	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs7309390	0.97[ASN][1000 genomes]
rs7314638	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap]
rs7316149	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7316734	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7397990	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7955203	0.93[ASN][1000 genomes]
rs7959238	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964138	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7966094	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972728	0.85[ASN][1000 genomes]
rs9705654	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9988963	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap]

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	nsv1054458	chr12:123045662-123133545	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7954006	B3GNT4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123077400-123137600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:123111600-123136200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:123120200-123140800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:123128200-123147600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:123128600-123133400	Weak transcription	HepG2	liver
6	chr12:123128800-123136200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:123130000-123135400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:123130600-123132800	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:123131000-123132000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:123131000-123132000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr12:123131000-123132200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:123131000-123132600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:123131200-123132000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr12:123131200-123132000	Active TSS	Primary B cells from cord blood	blood
15	chr12:123131200-123132400	Flanking Active TSS	GM12878-XiMat	blood
16	chr12:123131400-123132000	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr12:123131600-123132000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:123131600-123132000	Active TSS	Duodenum Mucosa	Duodenum
19	chr12:123131600-123132000	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr12:123131600-123132200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr12:123131600-123132400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr12:123131600-123132400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr12:123131800-123136200	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links