Variant report

Variant	rs1491983
Chromosome Location	chr3:49639803-49639804
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49456240..49456810-chr3:49639199..49640096,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145020	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1009051	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10452032	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs1078341	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs10865956	0.82[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs11130207	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130208	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11130211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130217	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap]
rs11709734	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs11720705	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs11721148	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928090	1.00[CHB][hapmap]
rs12583	0.82[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs12637313	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12715437	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap]
rs13096474	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap]
rs13096480	0.82[YRI][hapmap];0.89[AMR][1000 genomes]
rs13322887	0.82[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap]
rs1352889	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1464569	1.00[CHB][hapmap]
rs1491985	0.94[CEU][hapmap]
rs1532204	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1586827	0.94[CEU][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs1982861	0.82[ASW][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs2029591	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2131108	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs2312462	0.82[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs2329021	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs3020779	0.93[CEU][hapmap]
rs34890793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap]
rs3866330	1.00[CHB][hapmap];0.82[LWK][hapmap];0.95[MKK][hapmap]
rs3905330	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.95[MKK][hapmap]
rs4241405	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4241407	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs4855833	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4855845	0.94[CEU][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes]
rs4855846	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs4855848	0.86[AMR][1000 genomes]
rs4855849	0.89[AMR][1000 genomes]
rs4855882	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs4855885	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs6446284	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6446285	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6446286	0.82[AMR][1000 genomes]
rs6774202	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs6797299	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6805609	1.00[CHD][hapmap]
rs6809879	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap]
rs7613603	0.94[CEU][hapmap]
rs7620848	0.92[CEU][hapmap];0.87[YRI][hapmap]
rs7622786	1.00[ASN][1000 genomes]
rs7628207	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs7637711	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap]
rs7644148	0.82[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap]
rs7653505	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MKK][hapmap];1.00[ASN][1000 genomes]
rs8897	0.82[ASW][hapmap];1.00[CHD][hapmap]
rs940045	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap]
rs9824435	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs9829155	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap]
rs9830730	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs9835157	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap]
rs9849038	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs9860055	0.82[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap]
rs9862534	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap]
rs9870755	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap]
rs9870858	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs9871024	0.82[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.95[MKK][hapmap]
rs9883000	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1491983	DALRD3	cis	parietal	SCAN
rs1491983	AMT	cis	cerebellum	SCAN
rs1491983	WDR6	cis	cerebellum	SCAN
rs1491983	P4HTM	cis	parietal	SCAN
rs1491983	LZTFL1	cis	cerebellum	SCAN
rs1491983	NME6	cis	cerebellum	SCAN
rs1491983	GMPPB	cis	parietal	SCAN
rs1491983	AMT	cis	parietal	SCAN
rs1491983	ZNF589	cis	parietal	SCAN
rs1491983	DALRD3	cis	cerebellum	SCAN
rs1491983	GNL3	cis	cerebellum	SCAN
rs1491983	QRICH1	cis	cerebellum	SCAN
rs1491983	AMT	cis	Thyroid	GTEx
rs1491983	AMT	cis	Nerve Tibial	GTEx
rs1491983	RNF123	cis	parietal	SCAN
rs1491983	ARIH2	cis	cerebellum	SCAN
rs1491983	NICN1	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49637400-49640000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:49637400-49640600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:49637800-49653600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49638000-49644600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:49638000-49647200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:49638800-49640200	Weak transcription	Brain Angular Gyrus	brain
7	chr3:49639200-49643800	Weak transcription	Brain Anterior Caudate	brain
8	chr3:49639400-49640600	Enhancers	Placenta	Placenta
9	chr3:49639400-49641200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:49639600-49640400	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:49639600-49640600	Enhancers	Hela-S3	cervix
12	chr3:49639600-49640800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:49639600-49641200	Enhancers	HMEC	breast
14	chr3:49639600-49641200	Enhancers	NHEK	skin
15	chr3:49639600-49641400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:49639600-49641600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:49639800-49640200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:49639800-49644000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:49639800-49644000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:49639800-49644600	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links