Variant report

Variant	rs1466941
Chromosome Location	chr3:143670131-143670132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143604467..143605336-chr3:143669926..143671031,5	MCF-7	breast:
2	chr3:143669131..143673434-chr3:143689474..143692408,5	MCF-7	breast:
3	chr3:143604403..143605317-chr3:143669942..143670478,2	K562	blood:
4	chr3:143494312..143494922-chr3:143669977..143670492,2	MCF-7	breast:
5	chr3:143614293..143615305-chr3:143670036..143670705,3	MCF-7	breast:
6	chr3:143668700..143672507-chr3:143690640..143693277,4	K562	blood:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1025984	0.96[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs10513234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10513235	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs13064130	0.91[ASN][1000 genomes]
rs13068298	0.93[GIH][hapmap]
rs13078840	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs13081286	0.96[CEU][hapmap]
rs13086088	0.95[CEU][hapmap]
rs17602500	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17667256	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs1979910	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap]
rs1992093	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279856	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2885197	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34038325	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34071449	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34402874	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35072578	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35211123	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35362423	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35692092	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35716467	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4315684	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4446205	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4535221	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4563409	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59287916	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60505453	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62267390	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440210	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs6767236	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs6768153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804060	0.91[GIH][hapmap]
rs721572	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap]
rs723491	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7610378	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap]
rs7634145	0.96[CEU][hapmap]
rs7637912	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1466941	TM4SF18	cis	cerebellum	SCAN
rs1466941	HPS3	cis	cerebellum	SCAN
rs1466941	C3orf58	cis	cerebellum	SCAN
rs1466941	CHST2	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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