Variant report

Variant	rs12467407
Chromosome Location	chr2:30507340-30507341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30453318..30455814-chr2:30506103..30509890,3	K562	blood:
2	chr2:30492609..30498339-chr2:30504357..30508206,5	K562	blood:
3	chr2:30505644..30508835-chr2:30513800..30516199,3	K562	blood:
4	chr2:30454218..30456365-chr2:30505974..30508839,2	K562	blood:
5	chr2:30502244..30505490-chr2:30505646..30508832,3	K562	blood:
6	chr2:30497560..30499360-chr2:30505202..30507346,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213626	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10171296	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10171305	1.00[CHB][hapmap]
rs1039835	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1039836	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11127264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678385	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12467372	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12988733	1.00[ASN][1000 genomes]
rs17009315	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs57667995	0.91[ASN][1000 genomes]
rs6723650	0.90[ASN][1000 genomes]
rs6733372	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs7604484	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9558	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9967884	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12467407	HADHB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30487200-30517800	Enhancers	Primary B cells from peripheral blood	blood
2	chr2:30496400-30509800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:30496600-30524200	Weak transcription	Right Atrium	heart
4	chr2:30497800-30516400	Weak transcription	Gastric	stomach
5	chr2:30499800-30510400	Weak transcription	Aorta	Aorta
6	chr2:30501400-30510800	Enhancers	Primary B cells from cord blood	blood
7	chr2:30501800-30511000	Weak transcription	HSMM	muscle
8	chr2:30502000-30510000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:30502200-30509800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:30503800-30513800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:30504600-30510000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:30505800-30510000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:30506000-30509800	Weak transcription	Fetal Thymus	thymus
14	chr2:30506200-30509600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:30506200-30509600	Weak transcription	GM12878-XiMat	blood
16	chr2:30506400-30509600	Weak transcription	Primary T cells from cord blood	blood
17	chr2:30506400-30510000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:30506600-30510000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:30506800-30507600	Enhancers	Left Ventricle	heart
20	chr2:30506800-30507600	Enhancers	Right Ventricle	heart
21	chr2:30506800-30507800	Enhancers	NHDF-Ad	bronchial
22	chr2:30507000-30507600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:30507000-30516000	Weak transcription	Spleen	Spleen
24	chr2:30507200-30507400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:30507200-30507600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:30507200-30507600	Enhancers	Fetal Muscle Trunk	muscle
27	chr2:30507200-30507600	Flanking Active TSS	K562	blood
28	chr2:30507200-30507600	Enhancers	NHLF	lung
29	chr2:30507200-30510000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links