Variant report

Variant	rs1789896
Chromosome Location	chr4:100256984-100256985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:100249625..100252451-chr4:100254684..100257121,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs11499823	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs11499826	1.00[ASN][1000 genomes]
rs1154433	0.97[ASN][1000 genomes]
rs1154435	1.00[ASN][1000 genomes]
rs1154438	1.00[ASN][1000 genomes]
rs1154439	1.00[ASN][1000 genomes]
rs1154440	1.00[ASN][1000 genomes]
rs1154442	1.00[ASN][1000 genomes]
rs1154444	1.00[ASN][1000 genomes]
rs1154445	1.00[ASN][1000 genomes]
rs1154447	1.00[ASN][1000 genomes]
rs11936869	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1229851	1.00[ASN][1000 genomes]
rs1229854	1.00[ASN][1000 genomes]
rs1229855	1.00[ASN][1000 genomes]
rs1229856	1.00[ASN][1000 genomes]
rs1229857	1.00[ASN][1000 genomes]
rs1229858	1.00[ASN][1000 genomes]
rs1229973	1.00[ASN][1000 genomes]
rs1229978	0.97[ASN][1000 genomes]
rs1234584	1.00[ASN][1000 genomes]
rs1235415	0.97[ASN][1000 genomes]
rs1238015	0.97[ASN][1000 genomes]
rs1442479	0.97[ASN][1000 genomes]
rs1442480	0.97[ASN][1000 genomes]
rs1442481	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1583974	1.00[ASN][1000 genomes]
rs1612735	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1614972	0.83[GIH][hapmap]
rs1625439	0.97[ASN][1000 genomes]
rs1629270	0.97[ASN][1000 genomes]
rs1629838	1.00[ASN][1000 genomes]
rs1631460	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs1662020	1.00[ASN][1000 genomes]
rs1662021	1.00[ASN][1000 genomes]
rs1662031	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1662033	0.82[LWK][hapmap]
rs1662039	1.00[ASN][1000 genomes]
rs1662048	1.00[ASN][1000 genomes]
rs1662049	1.00[ASN][1000 genomes]
rs1662051	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs1662052	0.97[ASN][1000 genomes]
rs1662053	0.97[ASN][1000 genomes]
rs1662057	0.97[ASN][1000 genomes]
rs1662058	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1662059	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1662060	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1693424	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs1693425	0.97[ASN][1000 genomes]
rs1693426	0.97[ASN][1000 genomes]
rs1693427	0.97[ASN][1000 genomes]
rs1693428	0.95[ASN][1000 genomes]
rs1693430	0.97[ASN][1000 genomes]
rs1693431	0.97[ASN][1000 genomes]
rs1693456	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1693469	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1693470	1.00[ASN][1000 genomes]
rs1693471	0.95[ASN][1000 genomes]
rs1693476	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1693477	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1693480	0.97[ASN][1000 genomes]
rs1693481	0.97[ASN][1000 genomes]
rs1693482	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1693483	0.97[ASN][1000 genomes]
rs17586163	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs1789892	0.97[ASN][1000 genomes]
rs1789898	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1789900	0.97[ASN][1000 genomes]
rs1789902	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1789903	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1789906	0.97[ASN][1000 genomes]
rs1789908	0.97[ASN][1000 genomes]
rs1789910	0.97[ASN][1000 genomes]
rs1789911	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs1789912	0.97[ASN][1000 genomes]
rs1789913	0.97[ASN][1000 genomes]
rs1789914	0.97[ASN][1000 genomes]
rs1789916	0.97[ASN][1000 genomes]
rs1789917	0.97[ASN][1000 genomes]
rs1789919	0.97[ASN][1000 genomes]
rs1789920	0.82[LWK][hapmap]
rs1789921	0.82[LWK][hapmap]
rs1789924	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs1789925	1.00[ASN][1000 genomes]
rs2213041	1.00[CHB][hapmap]
rs2298753	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs2298755	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2453980	1.00[ASN][1000 genomes]
rs2584453	1.00[ASN][1000 genomes]
rs283408	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283415	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851299	0.97[ASN][1000 genomes]
rs2851300	1.00[ASN][1000 genomes]
rs3114048	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3811802	0.86[JPT][hapmap]
rs4093924	1.00[ASN][1000 genomes]
rs62307297	0.97[ASN][1000 genomes]
rs62307298	0.97[ASN][1000 genomes]
rs698	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs904093	0.97[ASN][1000 genomes]
rs904094	0.97[ASN][1000 genomes]
rs904095	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs904096	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs980972	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1014237	chr4:100102701-100365700	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv999549	chr4:100121609-100351749	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3353320	chr4:100147870-100425701	Genic enhancers ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv3394995	chr4:100147890-100425671	Enhancers Genic enhancers Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3387812	chr4:100232775-100261923	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1002809	chr4:100234048-100285508	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv3394945	chr4:100237238-100266245	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv3465817	chr4:100238736-100267823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3465818	chr4:100238736-100267823	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1789896	C4orf37	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100245800-100274200	Weak transcription	Pancreas	Pancrea
2	chr4:100251400-100259800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr4:100251400-100259800	Weak transcription	Fetal Lung	lung
4	chr4:100251400-100272800	Weak transcription	Adipose Nuclei	Adipose
5	chr4:100255000-100260400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:100255200-100257000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:100256200-100261200	Weak transcription	Fetal Intestine Large	intestine
8	chr4:100256200-100267800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:100256600-100257800	Weak transcription	Liver	Liver

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