Variant report

Variant	rs2100237
Chromosome Location	chr4:121747335-121747336
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	chr4:121745652..121748462-chr4:121750150..121752192,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10026047	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10033707	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10518379	0.83[CEU][hapmap]
rs10857072	0.94[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs11098589	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728387	0.83[CEU][hapmap]
rs11733915	0.80[CEU][hapmap]
rs11734461	0.81[CEU][hapmap]
rs11735169	0.82[CEU][hapmap]
rs12499000	0.83[CEU][hapmap]
rs12507922	0.83[CEU][hapmap]
rs12507970	0.81[CEU][hapmap]
rs12508015	0.83[CEU][hapmap]
rs12508048	0.83[CEU][hapmap]
rs12508821	0.83[CEU][hapmap]
rs12509870	0.88[CEU][hapmap]
rs12509912	0.83[CEU][hapmap]
rs12509939	0.83[CEU][hapmap]
rs12509993	0.86[CEU][hapmap]
rs1349347	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1376099	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1397770	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1450462	0.92[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1511302	0.82[LWK][hapmap]
rs1511303	0.83[CEU][hapmap]
rs1511307	0.83[CEU][hapmap]
rs1511309	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17051263	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868715	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1877214	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1877215	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1912720	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1949110	0.81[CEU][hapmap]
rs1949111	0.82[CEU][hapmap]
rs1987468	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2136997	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2203060	0.83[CEU][hapmap]
rs2221814	0.83[CEU][hapmap]
rs2221815	0.83[CEU][hapmap]
rs237212	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2597536	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597540	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2667172	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831670	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28850273	0.83[EUR][1000 genomes]
rs343181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs343184	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs343190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343192	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3761721	0.83[CEU][hapmap]
rs3789141	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789142	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804167	0.83[CEU][hapmap]
rs3804171	0.83[CEU][hapmap]
rs3804174	0.93[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4336252	0.83[CEU][hapmap]
rs4833178	0.83[CEU][hapmap]
rs4833179	0.83[CEU][hapmap]
rs4833180	0.83[CEU][hapmap]
rs4833181	0.83[CEU][hapmap]
rs4833183	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4833184	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4833674	0.82[CEU][hapmap]
rs4833675	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4833676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4833677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4833679	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4833680	0.83[CEU][hapmap]
rs4833681	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4833686	0.83[CEU][hapmap]
rs57841364	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59085467	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59837089	0.81[EUR][1000 genomes]
rs6835471	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs729934	0.83[CEU][hapmap]
rs896060	0.82[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879852	chr4:121108734-121768496	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv916737	chr4:121589793-121748847	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv461634	chr4:121623057-121765527	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv595334	chr4:121623057-121765527	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1013704	chr4:121657648-121791601	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
7	nsv879855	chr4:121691899-121747335	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv879857	chr4:121697932-121747335	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv879858	chr4:121703336-121747335	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121729600-121770400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:121730200-121753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:121730400-121760000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:121730400-121760800	Weak transcription	Pancreas	Pancrea
5	chr4:121731200-121752400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:121732000-121747600	Weak transcription	Fetal Lung	lung
7	chr4:121732200-121754800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:121737400-121751400	Weak transcription	Psoas Muscle	Psoas
9	chr4:121737600-121759800	Weak transcription	Lung	lung
10	chr4:121737800-121754400	Weak transcription	Aorta	Aorta
11	chr4:121738200-121759600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:121738800-121750600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:121743600-121750000	Weak transcription	Fetal Heart	heart
14	chr4:121743800-121765400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:121745200-121751400	Weak transcription	Left Ventricle	heart
16	chr4:121746200-121748000	Enhancers	Fetal Intestine Small	intestine
17	chr4:121746600-121748000	Enhancers	Ovary	ovary
18	chr4:121746800-121747800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:121746800-121748400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr4:121747200-121747600	Enhancers	Spleen	Spleen
21	chr4:121747200-121755400	Weak transcription	Fetal Intestine Large	intestine

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