Variant report

Variant	rs1229979
Chromosome Location	chr4:100255953-100255954
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	chr4:100249625..100252451-chr4:100254684..100257121,2	MCF-7	breast:

Extended variants
information (count: 145 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1154433	0.91[AFR][1000 genomes]
rs1154434	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1154435	0.94[AFR][1000 genomes]
rs1154436	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1154437	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1154438	0.88[AFR][1000 genomes]
rs1154439	0.94[AFR][1000 genomes]
rs1154440	0.94[AFR][1000 genomes]
rs1154441	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1154442	0.94[AFR][1000 genomes]
rs1154443	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1154444	0.94[AFR][1000 genomes]
rs1154445	0.94[AFR][1000 genomes]
rs1154446	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1154447	0.94[AFR][1000 genomes]
rs1229849	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1229851	0.94[AFR][1000 genomes]
rs1229853	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1229854	0.94[AFR][1000 genomes]
rs1229855	0.94[AFR][1000 genomes]
rs1229856	0.94[AFR][1000 genomes]
rs1229857	0.94[AFR][1000 genomes]
rs1229858	0.94[AFR][1000 genomes]
rs1229859	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1229860	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1229862	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1229973	0.94[AFR][1000 genomes]
rs1229978	0.94[AFR][1000 genomes]
rs1234584	0.89[AFR][1000 genomes]
rs1235415	0.94[AFR][1000 genomes]
rs1238015	0.83[AFR][1000 genomes]
rs1442479	0.94[AFR][1000 genomes]
rs1442480	0.94[AFR][1000 genomes]
rs1442481	0.94[AFR][1000 genomes]
rs1583974	0.94[AFR][1000 genomes]
rs1612735	0.94[AFR][1000 genomes]
rs1614377	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1625439	0.94[AFR][1000 genomes]
rs1629270	0.94[AFR][1000 genomes]
rs1629838	0.94[AFR][1000 genomes]
rs1631460	0.83[ASW][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1662020	0.94[AFR][1000 genomes]
rs1662021	0.94[AFR][1000 genomes]
rs1662031	0.94[AFR][1000 genomes]
rs1662033	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662036	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1662037	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1662039	0.89[AFR][1000 genomes]
rs1662045	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1662047	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1662048	0.96[AFR][1000 genomes]
rs1662049	0.94[AFR][1000 genomes]
rs1662051	0.83[ASW][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs1662052	0.94[AFR][1000 genomes]
rs1662053	0.89[AFR][1000 genomes]
rs1662055	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662056	1.00[ASN][1000 genomes]
rs1662057	0.94[AFR][1000 genomes]
rs1662058	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1662059	0.94[AFR][1000 genomes]
rs1662060	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1693424	0.83[ASW][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1693425	0.94[AFR][1000 genomes]
rs1693426	0.94[AFR][1000 genomes]
rs1693427	0.94[AFR][1000 genomes]
rs1693428	0.81[AFR][1000 genomes]
rs1693430	0.94[AFR][1000 genomes]
rs1693431	0.94[AFR][1000 genomes]
rs1693448	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1693454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1693456	0.94[AFR][1000 genomes]
rs1693468	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1693469	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1693470	0.94[AFR][1000 genomes]
rs1693471	0.94[AFR][1000 genomes]
rs1693476	0.83[ASW][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1693477	0.94[AFR][1000 genomes]
rs1693480	0.94[AFR][1000 genomes]
rs1693481	0.94[AFR][1000 genomes]
rs1693482	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1693483	0.94[AFR][1000 genomes]
rs17028821	0.85[YRI][hapmap]
rs1789892	0.91[AFR][1000 genomes]
rs1789895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789898	0.92[LWK][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes]
rs1789900	0.91[AFR][1000 genomes]
rs1789901	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789902	0.94[AFR][1000 genomes]
rs1789903	0.83[ASW][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1789904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789906	0.94[AFR][1000 genomes]
rs1789908	0.94[AFR][1000 genomes]
rs1789910	0.94[AFR][1000 genomes]
rs1789911	0.83[ASW][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1789912	0.94[AFR][1000 genomes]
rs1789913	0.94[AFR][1000 genomes]
rs1789914	0.87[AFR][1000 genomes]
rs1789915	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789916	0.94[AFR][1000 genomes]
rs1789917	0.94[AFR][1000 genomes]
rs1789919	0.94[AFR][1000 genomes]
rs1789920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789923	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789924	0.83[ASW][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1789925	0.94[AFR][1000 genomes]
rs2298755	0.83[ASW][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2453980	0.89[AFR][1000 genomes]
rs2584453	0.94[AFR][1000 genomes]
rs2584455	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs283415	0.85[LWK][hapmap]
rs2851299	0.88[AFR][1000 genomes]
rs2851300	0.94[AFR][1000 genomes]
rs2866152	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3114048	0.94[AFR][1000 genomes]
rs3133158	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35348915	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35380107	0.89[ASN][1000 genomes]
rs36070167	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3846448	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4093924	0.94[AFR][1000 genomes]
rs62307297	0.94[AFR][1000 genomes]
rs62307298	0.94[AFR][1000 genomes]
rs698	0.83[ASW][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs71612681	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71612682	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs904093	0.94[AFR][1000 genomes]
rs904094	0.94[AFR][1000 genomes]
rs904095	0.83[ASW][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs904096	0.83[ASW][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs980972	0.94[AFR][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

No data

Chromatin state (count:7 , 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	chr4:100255600-100256600	Enhancers	Liver	Liver

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