Variant report

Variant	rs2884028
Chromosome Location	chr2:172455639-172455640
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172440684..172442234-chr2:172455013..172456905,2	MCF-7	breast:
2	chr2:172454966..172455847-chr2:172978063..172978629,2	K562	blood:
3	chr2:172454209..172457044-chr2:172571141..172573301,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077380	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10185715	0.87[ASN][1000 genomes]
rs10211146	0.89[ASN][1000 genomes]
rs10221787	0.89[ASN][1000 genomes]
rs10432421	0.85[ASN][1000 genomes]
rs10432422	0.85[ASN][1000 genomes]
rs10432469	0.84[ASN][1000 genomes]
rs10432470	0.86[ASN][1000 genomes]
rs10432471	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10432472	0.85[ASN][1000 genomes]
rs10432473	0.86[ASN][1000 genomes]
rs10930485	0.92[ASN][1000 genomes]
rs10930486	0.82[ASN][1000 genomes]
rs11674857	0.84[ASN][1000 genomes]
rs11680728	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11680862	0.92[ASN][1000 genomes]
rs11680897	0.92[ASN][1000 genomes]
rs11683752	0.92[ASN][1000 genomes]
rs11683762	0.88[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs11686621	0.92[ASN][1000 genomes]
rs11689452	0.83[ASN][1000 genomes]
rs11689637	0.93[ASN][1000 genomes]
rs11693157	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12472229	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12476299	0.88[ASN][1000 genomes]
rs12618717	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12622021	0.84[ASN][1000 genomes]
rs12991896	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12996145	0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12997634	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13002792	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13016328	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13024519	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13025303	0.94[ASN][1000 genomes]
rs13025856	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1399960	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1473995	0.83[ASW][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1533417	0.84[ASN][1000 genomes]
rs1543128	0.85[ASN][1000 genomes]
rs1554157	0.86[ASN][1000 genomes]
rs1554158	0.86[ASN][1000 genomes]
rs1606926	0.82[ASN][1000 genomes]
rs1807872	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1969271	0.86[ASN][1000 genomes]
rs1996268	0.84[ASN][1000 genomes]
rs2037158	0.85[ASN][1000 genomes]
rs2037159	0.85[ASN][1000 genomes]
rs2037160	0.82[ASN][1000 genomes]
rs2037161	0.85[ASN][1000 genomes]
rs2037163	0.84[ASN][1000 genomes]
rs2102739	0.82[ASN][1000 genomes]
rs2102740	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2138350	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2176150	0.86[ASN][1000 genomes]
rs2356796	0.85[ASN][1000 genomes]
rs2356797	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28893802	0.86[ASN][1000 genomes]
rs34054455	0.81[ASN][1000 genomes]
rs34919335	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35735503	0.81[ASN][1000 genomes]
rs4264541	0.83[ASN][1000 genomes]
rs4265979	0.86[ASN][1000 genomes]
rs4265980	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4667691	0.90[ASN][1000 genomes]
rs4668391	0.86[ASN][1000 genomes]
rs4668392	0.89[ASN][1000 genomes]
rs4668393	0.94[ASN][1000 genomes]
rs4668394	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs4668395	0.85[ASN][1000 genomes]
rs4668396	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57130402	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59567105	0.84[ASN][1000 genomes]
rs6433301	0.86[ASN][1000 genomes]
rs6433302	0.86[ASN][1000 genomes]
rs6433305	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6704691	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6711201	0.89[ASN][1000 genomes]
rs6718546	0.86[ASN][1000 genomes]
rs6723896	0.86[ASN][1000 genomes]
rs6725338	0.86[ASN][1000 genomes]
rs6743208	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6747069	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6747775	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6754595	0.86[ASN][1000 genomes]
rs7562302	0.86[ASN][1000 genomes]
rs7571192	0.85[ASN][1000 genomes]
rs7575168	0.84[ASN][1000 genomes]
rs7592639	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7606149	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7606189	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7606481	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs908371	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9287946	0.84[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs9678221	0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs997635	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[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	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv997638	chr2:172442205-172560406	Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2884028	ZAK	cis	parietal	SCAN
rs2884028	CD226	trans	cerebellum	SCAN
rs2884028	B3GALT1	cis	parietal	SCAN
rs2884028	CHN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172453000-172455800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:172453200-172455800	Weak transcription	NHEK	skin
3	chr2:172455200-172457400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:172455400-172455800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:172455400-172455800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:172455400-172455800	Active TSS	Brain Hippocampus Middle	brain
7	chr2:172455400-172455800	Enhancers	K562	blood
8	chr2:172455600-172455800	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:172455600-172455800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr2:172455600-172455800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:172455600-172455800	Enhancers	Adipose Nuclei	Adipose
12	chr2:172455600-172455800	Enhancers	Brain Angular Gyrus	brain
13	chr2:172455600-172455800	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr2:172455600-172455800	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr2:172455600-172455800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
16	chr2:172455600-172455800	Enhancers	A549	lung
17	chr2:172455600-172455800	Flanking Active TSS	NHDF-Ad	bronchial
18	chr2:172455600-172455800	Enhancers	NHLF	lung
19	chr2:172455600-172455800	Enhancers	Osteobl	bone
20	chr2:172455600-172457200	Enhancers	HMEC	breast
21	chr2:172455600-172457600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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