Variant report

Variant	rs4076678
Chromosome Location	chr1:172024528-172024529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10157345	0.81[ASN][1000 genomes]
rs10218612	1.00[JPT][hapmap]
rs10489730	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs10797716	0.97[ASN][1000 genomes]
rs10797719	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs10797720	0.98[ASN][1000 genomes]
rs10797725	0.98[ASN][1000 genomes]
rs10797734	0.81[ASN][1000 genomes]
rs10797735	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10797736	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10910938	0.92[EUR][1000 genomes]
rs10910939	0.81[ASN][1000 genomes]
rs10910945	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10910966	1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs10910968	0.81[ASN][1000 genomes]
rs10910969	0.81[ASN][1000 genomes]
rs10910970	0.81[ASN][1000 genomes]
rs10911109	0.94[JPT][hapmap]
rs10911112	0.94[JPT][hapmap]
rs10911121	0.81[JPT][hapmap]
rs12027295	0.81[ASN][1000 genomes]
rs12028055	0.81[ASN][1000 genomes]
rs12037820	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12037831	0.81[ASN][1000 genomes]
rs12038713	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12047492	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs12117623	0.82[EUR][1000 genomes]
rs12119190	0.80[EUR][1000 genomes]
rs12120556	0.94[JPT][hapmap]
rs12128720	0.97[ASN][1000 genomes]
rs1555382	0.98[ASN][1000 genomes]
rs1555383	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2038481	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs2057302	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2057303	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2181624	0.94[JPT][hapmap]
rs2208367	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2295610	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2295611	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36178280	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36180993	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736791	1.00[JPT][hapmap]
rs4333881	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4489594	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916241	0.98[ASN][1000 genomes]
rs4916413	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425599	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425600	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6669406	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6683503	0.98[ASN][1000 genomes]
rs6700538	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518865	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7519236	0.98[ASN][1000 genomes]
rs7520595	0.81[ASN][1000 genomes]
rs7530970	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7533694	1.00[CEU][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9286842	1.00[JPT][hapmap];0.83[MEX][hapmap]

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	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	nsv3532	chr1:171997451-172042351	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4076678	SPINT2	trans	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172006400-172025600	Weak transcription	Adipose Nuclei	Adipose
2	chr1:172010600-172051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:172010800-172037600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:172011400-172037800	Weak transcription	Ovary	ovary
5	chr1:172015000-172033200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:172015000-172042600	Weak transcription	Fetal Brain Female	brain
7	chr1:172015200-172026000	Weak transcription	Aorta	Aorta
8	chr1:172015200-172032400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:172016600-172037800	Weak transcription	Brain Substantia Nigra	brain
10	chr1:172020200-172038800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:172020200-172040600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:172021400-172026600	Weak transcription	Left Ventricle	heart
13	chr1:172023400-172024600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:172024200-172024600	Strong transcription	Brain Anterior Caudate	brain
15	chr1:172024200-172025200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:172024200-172025200	Strong transcription	Brain Hippocampus Middle	brain
17	chr1:172024200-172025400	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr1:172024400-172024800	Strong transcription	Brain Germinal Matrix	brain
19	chr1:172024400-172025200	Strong transcription	Brain Cingulate Gyrus	brain

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