Variant report

Variant	rs481746
Chromosome Location	chr1:225750889-225750890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225746985..225751093-chr1:225752796..225757571,6	MCF-7	breast:
2	chr1:225749423..225753817-chr1:225762861..225765930,3	K562	blood:
3	chr1:225749504..225751899-chr1:225752062..225754105,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10799320	0.85[AMR][1000 genomes]
rs12034829	0.82[AMR][1000 genomes]
rs12071529	0.84[AFR][1000 genomes]
rs1222434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1222439	0.81[EUR][1000 genomes]
rs1336480	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360958	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629896	0.88[TSI][hapmap]
rs1764345	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1764347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1771318	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1891000	0.82[AMR][1000 genomes]
rs2035916	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3904084	1.00[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs475794	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs499385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499782	0.80[AMR][1000 genomes]
rs516323	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525062	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526221	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566085	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59363938	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6426075	0.89[TSI][hapmap]
rs7529690	0.82[AMR][1000 genomes]
rs7545317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9651009	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs481746	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225707200-225755000	Weak transcription	Gastric	stomach
2	chr1:225717800-225758200	Weak transcription	HepG2	liver
3	chr1:225718400-225756400	Weak transcription	NHLF	lung
4	chr1:225727600-225753600	Weak transcription	NHEK	skin
5	chr1:225728000-225753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:225730200-225753400	Weak transcription	NHDF-Ad	bronchial
7	chr1:225730200-225753600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
10	chr1:225732400-225763000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:225734600-225763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:225736600-225753400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:225736600-225756200	Weak transcription	HSMMtube	muscle
14	chr1:225737800-225756400	Weak transcription	Right Ventricle	heart
15	chr1:225738000-225753600	Weak transcription	Aorta	Aorta
16	chr1:225738000-225753600	Weak transcription	Ovary	ovary
17	chr1:225738200-225753400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:225738600-225758000	Weak transcription	Brain Germinal Matrix	brain
19	chr1:225739800-225753200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:225739800-225754000	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:225741800-225758600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:225742800-225753600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:225744800-225759400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:225744800-225760200	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:225744800-225761400	Weak transcription	Brain Angular Gyrus	brain
26	chr1:225744800-225768200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:225744800-225768600	Weak transcription	Fetal Brain Male	brain
28	chr1:225745000-225753400	Weak transcription	Adipose Nuclei	Adipose
29	chr1:225745000-225760800	Weak transcription	Fetal Kidney	kidney
30	chr1:225745000-225770000	Weak transcription	HUVEC	blood vessel
31	chr1:225745000-225772800	Weak transcription	Fetal Brain Female	brain
32	chr1:225745200-225753400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:225745400-225753400	Weak transcription	Left Ventricle	heart
34	chr1:225745400-225753400	Weak transcription	Psoas Muscle	Psoas
35	chr1:225745400-225755800	Weak transcription	Fetal Intestine Large	intestine
36	chr1:225745800-225755000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:225746000-225753600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:225746200-225753600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:225746200-225756200	Weak transcription	Fetal Heart	heart
40	chr1:225746600-225755600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:225746600-225756400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:225747200-225759800	Weak transcription	Brain Substantia Nigra	brain
43	chr1:225747400-225752000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:225747600-225752000	Strong transcription	Osteobl	bone
45	chr1:225747800-225751000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:225747800-225753600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:225747800-225753600	Weak transcription	HSMM	muscle
48	chr1:225747800-225753800	Weak transcription	Hela-S3	cervix
49	chr1:225747800-225755400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:225747800-225755800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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