Variant report

Variant	rs4972839
Chromosome Location	chr2:173410860-173410861
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173331974..173332821-chr2:173410140..173411046,3	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10497383	0.93[CEU][hapmap]
rs10497384	0.93[CEU][hapmap]
rs1076595	0.82[JPT][hapmap]
rs10930558	0.82[CEU][hapmap]
rs11883720	0.93[CEU][hapmap]
rs11896937	0.93[CEU][hapmap]
rs11897024	0.93[CEU][hapmap]
rs12465295	0.82[JPT][hapmap]
rs12465442	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12467358	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12474168	0.86[ASN][1000 genomes]
rs12474995	0.86[ASN][1000 genomes]
rs12475916	0.84[ASN][1000 genomes]
rs12476126	0.83[ASN][1000 genomes]
rs12477247	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12477594	0.82[JPT][hapmap]
rs12478465	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12619242	0.86[ASN][1000 genomes]
rs12622687	0.86[ASN][1000 genomes]
rs13383151	0.86[ASN][1000 genomes]
rs13402061	0.86[ASN][1000 genomes]
rs1344272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1574247	0.86[ASN][1000 genomes]
rs1574258	0.93[CEU][hapmap]
rs16860543	0.81[ASN][1000 genomes]
rs17286988	0.93[CEU][hapmap]
rs17676773	0.93[CEU][hapmap]
rs17677404	0.93[CEU][hapmap]
rs17727678	0.93[CEU][hapmap]
rs17727732	0.93[CEU][hapmap]
rs17739735	0.93[CEU][hapmap]
rs17739946	0.93[CEU][hapmap]
rs2178474	0.86[ASN][1000 genomes]
rs2178475	0.93[CEU][hapmap]
rs2272498	0.93[CEU][hapmap]
rs2293646	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2293649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2357415	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs3792255	0.93[CEU][hapmap]
rs3792256	0.93[CEU][hapmap]
rs3792260	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs3828342	0.93[CEU][hapmap]
rs4308101	0.86[ASN][1000 genomes]
rs4619573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4972510	0.86[CEU][hapmap]
rs4972511	0.93[CEU][hapmap]
rs4972832	0.93[CEU][hapmap]
rs56084828	0.82[ASN][1000 genomes]
rs57957394	0.86[ASN][1000 genomes]
rs58016698	0.86[ASN][1000 genomes]
rs58044442	0.86[ASN][1000 genomes]
rs59020762	0.86[ASN][1000 genomes]
rs59524026	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59610589	0.86[ASN][1000 genomes]
rs60275829	0.82[ASN][1000 genomes]
rs60442917	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60446415	0.86[ASN][1000 genomes]
rs6433359	0.93[CEU][hapmap]
rs6433360	0.93[CEU][hapmap]
rs6715294	0.93[CEU][hapmap]
rs6718477	0.82[JPT][hapmap]
rs6728419	0.93[CEU][hapmap]
rs6731691	0.93[CEU][hapmap]
rs6746138	0.83[AFR][1000 genomes]
rs6755100	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6755605	0.93[CEU][hapmap]
rs72894386	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72894389	0.81[AFR][1000 genomes]
rs7564591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7564654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7565216	0.86[ASN][1000 genomes]
rs7582972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7591883	0.86[ASN][1000 genomes]
rs7609465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 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	chr2:173392600-173419600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:173399600-173414400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:173408800-173413800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr2:173410000-173418800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:173410400-173411000	ZNF genes & repeats	Primary T cells from cord blood	blood
6	chr2:173410400-173411200	ZNF genes & repeats	GM12878-XiMat	blood
7	chr2:173410600-173411000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr2:173410600-173411200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:173410600-173411400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:173410600-173411400	Enhancers	Placenta	Placenta
11	chr2:173410600-173413000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr2:173410600-173413400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr2:173410600-173413600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:173410600-173417000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:173410800-173413600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr2:173410800-173418000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:173410800-173418800	Weak transcription	Rectal Mucosa Donor 29	rectum

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