Variant report

Variant	rs4855833
Chromosome Location	chr3:49657441-49657442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49656466..49658161-chr3:49661338..49664301,2	MCF-7	breast:
2	chr3:49656091..49658798-chr3:49660626..49662270,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1009051	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10452032	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1078341	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865956	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs11130207	0.82[AMR][1000 genomes]
rs11130208	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs11130211	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130217	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs11709734	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11720705	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11721148	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928090	1.00[CHB][hapmap]
rs12583	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs12637313	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12715437	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs13096480	0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13322887	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap]
rs1352889	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463728	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1464569	1.00[CHB][hapmap]
rs1491983	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]
rs1491985	1.00[CEU][hapmap]
rs1532204	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs1586827	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1982861	1.00[CHD][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs2029591	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2131108	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2312462	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];0.83[YRI][hapmap]
rs2329021	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs34890793	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap]
rs3866330	1.00[CHB][hapmap];0.80[LWK][hapmap];0.95[MKK][hapmap]
rs3905330	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[LWK][hapmap];0.95[MKK][hapmap]
rs4241405	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs4241407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs4855845	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855846	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855848	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855849	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855882	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4855885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55754265	0.81[EUR][1000 genomes]
rs62262671	0.81[EUR][1000 genomes]
rs62262672	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62262673	0.97[EUR][1000 genomes]
rs62262675	0.98[EUR][1000 genomes]
rs6446284	0.84[AMR][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6446286	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6774202	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6797299	0.94[CEU][hapmap];0.84[AMR][1000 genomes]
rs6805609	1.00[CHD][hapmap]
rs6809879	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs7613603	1.00[CEU][hapmap]
rs7620848	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs7622786	1.00[ASN][1000 genomes]
rs7628207	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs7637711	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs7644148	1.00[CHD][hapmap];0.84[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	1.00[CHD][hapmap]
rs9824435	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9829155	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs9830730	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9835157	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs9849038	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9860055	1.00[CHD][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap]
rs9862534	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.95[MKK][hapmap]
rs9870755	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs9870858	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9871024	1.00[CHD][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap]
rs9883000	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	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
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4855833	AMT	cis	parietal	SCAN
rs4855833	RNF123	cis	Artery Tibial	GTEx
rs4855833	RNF123	cis	parietal	SCAN
rs4855833	AMT	cis	lung	GTEx
rs4855833	AMT	cis	Thyroid	GTEx
rs4855833	QRICH1	cis	cerebellum	SCAN
rs4855833	OR9G4	trans	parietal	SCAN
rs4855833	GMPPB	cis	parietal	SCAN
rs4855833	ZNF589	cis	parietal	SCAN
rs4855833	GNL3	cis	cerebellum	SCAN
rs4855833	P4HTM	cis	parietal	SCAN
rs4855833	DALRD3	cis	parietal	SCAN
rs4855833	DALRD3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49648400-49662000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:49654000-49662400	Weak transcription	Fetal Brain Female	brain
3	chr3:49654200-49662600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:49654400-49668200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:49654600-49662200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:49654600-49662400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49654600-49662600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49654600-49662600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:49654600-49663600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:49654600-49664200	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:49655000-49668800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:49655600-49676200	Weak transcription	HepG2	liver
13	chr3:49656000-49657600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:49656600-49657600	Enhancers	Brain Angular Gyrus	brain
15	chr3:49656800-49657600	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:49656800-49657600	Enhancers	HSMM	muscle
17	chr3:49657000-49657600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:49657000-49657600	Enhancers	Brain Substantia Nigra	brain
19	chr3:49657200-49662400	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:49657400-49658600	Weak transcription	NH-A	brain
21	chr3:49657400-49662200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:49657400-49662400	Weak transcription	Brain Inferior Temporal Lobe	brain

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