Variant report

Variant	rs331946
Chromosome Location	chr4:143680948-143680949
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	chr4:143391122..143393717-chr4:143678959..143680972,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10024696	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1017527	0.84[JPT][hapmap]
rs1031104	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10519666	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10857399	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11723982	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11724017	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11726381	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11943397	0.81[CHB][hapmap]
rs12509304	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12640389	0.82[ASN][1000 genomes]
rs12650777	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs13117185	0.83[ASN][1000 genomes]
rs1373030	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1373031	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1373034	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1441417	0.90[CHB][hapmap]
rs1443183	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1443187	0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[ASN][1000 genomes]
rs1465962	0.83[ASN][1000 genomes]
rs167960	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17016768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17016779	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17016789	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17732408	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17732791	0.81[AMR][1000 genomes]
rs1822360	0.83[ASN][1000 genomes]
rs1822361	0.83[ASN][1000 genomes]
rs1822362	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1838082	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1867214	0.83[ASN][1000 genomes]
rs1899565	0.81[CHB][hapmap]
rs1965828	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1992417	0.81[AMR][1000 genomes]
rs1992418	0.81[AMR][1000 genomes]
rs2120158	0.81[CHB][hapmap]
rs2165819	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2589994	0.83[ASN][1000 genomes]
rs3113593	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs331939	0.83[ASN][1000 genomes]
rs331940	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs331942	0.83[ASN][1000 genomes]
rs331943	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs331944	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331945	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs331947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331951	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs331952	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs331953	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331954	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331956	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331958	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331959	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331960	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331961	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34831472	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4690698	0.95[CEU][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs4690699	0.83[MEX][hapmap]
rs4690700	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4690725	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4690726	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4690727	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56011189	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56332157	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537129	1.00[CHB][hapmap]
rs6830053	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs6831562	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6839158	0.90[CHB][hapmap]
rs72728615	0.82[ASN][1000 genomes]
rs72728621	0.81[ASN][1000 genomes]
rs72728641	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72728649	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72728651	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72728654	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72728661	0.83[ASN][1000 genomes]
rs72728667	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72728681	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72728686	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7656375	1.00[CHB][hapmap]
rs7663475	1.00[CHB][hapmap]
rs7666140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7668552	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7668786	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7671783	0.84[JPT][hapmap]
rs7679151	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7695461	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7695514	0.91[JPT][hapmap]
rs978361	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830101	chr4:143518810-143684392	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv595606	chr4:143631691-143729595	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv880174	chr4:143639498-143848024	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs331946	C4orf49	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143672600-143698400	Weak transcription	Aorta	Aorta
2	chr4:143675400-143683000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:143675400-143688400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:143675600-143683600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:143679200-143682000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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