Variant report

Variant	rs9844482
Chromosome Location	chr3:178844004-178844005
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	chr3:178842346..178844303-chr3:179040865..179042396,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121864	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1059691	1.00[ASN][1000 genomes]
rs10936992	0.95[ASN][1000 genomes]
rs10936994	0.85[ASN][1000 genomes]
rs11706842	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs11708869	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1183319	0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11918324	0.88[ASN][1000 genomes]
rs11918587	0.90[ASN][1000 genomes]
rs11919383	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11922631	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11924545	0.81[ASN][1000 genomes]
rs11924547	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11924600	0.81[ASN][1000 genomes]
rs11925655	0.90[ASN][1000 genomes]
rs12488074	0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1568205	0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs17849071	0.88[ASN][1000 genomes]
rs1850504	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs1970901	0.82[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1976765	0.90[ASN][1000 genomes]
rs2865082	0.88[ASN][1000 genomes]
rs3729674	0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3729676	1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3729682	0.88[ASN][1000 genomes]
rs3729694	0.88[ASN][1000 genomes]
rs3960984	0.83[ASW][hapmap];1.00[CHB][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs3975510	0.85[ASN][1000 genomes]
rs3975513	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3976507	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs4080957	1.00[ASN][1000 genomes]
rs4855093	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4855095	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs55685804	0.88[ASN][1000 genomes]
rs55933053	0.90[ASN][1000 genomes]
rs55961756	0.88[ASN][1000 genomes]
rs56095736	1.00[ASN][1000 genomes]
rs56143971	0.88[ASN][1000 genomes]
rs56372555	0.90[ASN][1000 genomes]
rs56378415	0.86[ASN][1000 genomes]
rs59340081	0.90[ASN][1000 genomes]
rs59408989	0.95[ASN][1000 genomes]
rs59922883	0.90[ASN][1000 genomes]
rs61796482	0.88[ASN][1000 genomes]
rs61796483	0.81[ASN][1000 genomes]
rs62408837	0.93[ASN][1000 genomes]
rs6443619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6443624	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6443625	0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6443626	0.90[ASN][1000 genomes]
rs6443627	0.90[ASN][1000 genomes]
rs6443628	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6443629	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs67562832	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs67609137	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6765953	0.88[ASN][1000 genomes]
rs6767284	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6769154	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6769162	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6769508	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6770267	0.90[ASN][1000 genomes]
rs6771313	1.00[ASN][1000 genomes]
rs6774158	0.88[ASN][1000 genomes]
rs6777203	0.88[ASN][1000 genomes]
rs6782557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs6786049	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6786114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6791153	0.88[ASN][1000 genomes]
rs67920954	0.88[ASN][1000 genomes]
rs6792189	0.90[ASN][1000 genomes]
rs6794252	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6797304	0.90[ASN][1000 genomes]
rs6798817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs6799756	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs6803076	0.98[ASN][1000 genomes]
rs6803219	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6806555	0.90[ASN][1000 genomes]
rs6806917	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6810246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.90[ASN][1000 genomes]
rs73051974	0.90[ASN][1000 genomes]
rs73187264	0.88[ASN][1000 genomes]
rs73187276	0.88[ASN][1000 genomes]
rs7372645	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7612533	0.90[ASN][1000 genomes]
rs7614305	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7614418	0.88[ASN][1000 genomes]
rs7615076	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7621329	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7621436	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7623154	0.82[CHB][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs7624090	0.88[ASN][1000 genomes]
rs7627273	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7628855	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7635669	0.83[ASW][hapmap];1.00[CHB][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs7636454	0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs7638323	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs7638649	0.90[ASN][1000 genomes]
rs7641889	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs7641983	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7644648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7645550	0.86[CHD][hapmap]
rs7646409	0.83[ASW][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7648857	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7650809	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7651265	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs938752	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs9631497	0.86[ASN][1000 genomes]
rs9813190	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9819762	0.88[ASN][1000 genomes]
rs9829903	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9831234	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9833438	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838411	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9839519	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9841051	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9844270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9850621	0.90[ASN][1000 genomes]
rs9862294	0.90[ASN][1000 genomes]
rs9866361	0.83[ASW][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9877812	0.90[ASN][1000 genomes]
rs9881887	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv878037	chr3:178825910-178871906	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9844482	SOX2	cis	parietal	SCAN
rs9844482	C2orf69	trans	parietal	SCAN
rs9844482	KCNMB3	cis	lymphoblastoid	seeQTL

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

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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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