Variant report

Variant	rs28598872
Chromosome Location	chr2:20205848-20205849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20099721..20101368-chr2:20204158..20205910,2	K562	blood:
2	chr2:20203665..20207469-chr2:20209736..20214726,5	MCF-7	breast:
3	chr2:20203402..20205904-chr2:20205994..20208147,2	MCF-7	breast:
4	chr2:20188602..20191766-chr2:20204187..20206956,3	MCF-7	breast:
5	chr2:20205089..20207938-chr2:20214962..20217155,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118965	Chromatin interaction
ENSG00000227210	Chromatin interaction
ENSG00000132031	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10165128	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10178256	0.90[ASN][1000 genomes]
rs10187524	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10190308	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10191437	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10197369	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10495700	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1115274	0.84[ASN][1000 genomes]
rs12477955	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12478934	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12612708	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12616917	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1370587	0.85[EUR][1000 genomes]
rs1437859	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1595414	0.82[ASN][1000 genomes]
rs1824661	0.90[ASN][1000 genomes]
rs1947730	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2045779	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242192	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28401180	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731663	0.90[ASN][1000 genomes]
rs3820949	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4297843	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6721864	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6736663	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6741091	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7569975	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7572536	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7575732	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7584726	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7604699	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1005431	chr2:20174676-20210163	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20190400-20207400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:20190600-20211400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:20190800-20208400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:20191000-20211200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:20191400-20208000	Weak transcription	A549	lung
6	chr2:20200000-20206800	Weak transcription	HSMMtube	muscle
7	chr2:20200200-20211800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:20201800-20211400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:20201800-20212400	Weak transcription	Gastric	stomach
10	chr2:20202000-20210400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:20202400-20210200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:20203000-20206400	Genic enhancers	HepG2	liver
13	chr2:20203800-20206800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:20205000-20206200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:20205200-20206600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:20205600-20206000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:20205600-20206200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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