Variant report

Variant	rs28558133
Chromosome Location	chr6:26531433-26531434
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26530786..26533089-chr6:26568633..26571101,2	K562	blood:
2	chr6:26526578..26530250-chr6:26530283..26533379,3	MCF-7	breast:
3	chr6:26530090..26531605-chr6:26535958..26538607,2	MCF-7	breast:
4	chr6:26521199..26522704-chr6:26531334..26533280,2	MCF-7	breast:
5	chr6:26329107..26333235-chr6:26529334..26532709,3	K562	blood:
6	chr6:26526060..26529298-chr6:26530268..26533280,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261353	Chromatin interaction
ENSG00000228223	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1001687	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10214634	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10223789	0.87[AFR][1000 genomes]
rs10223792	0.86[AFR][1000 genomes]
rs10484442	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1056347	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056667	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056668	0.89[EUR][1000 genomes]
rs1078679	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10946834	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10946835	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10946837	0.86[EUR][1000 genomes]
rs11754138	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11756120	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12526680	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12663883	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12663894	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12665431	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1321479	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1321480	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1321481	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1321482	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1535274	0.80[AMR][1000 genomes]
rs1535276	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535277	0.85[AFR][1000 genomes]
rs1570059	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1570060	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1570061	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1884946	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884947	0.80[EUR][1000 genomes]
rs1884948	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1884949	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1977201	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2208331	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2224380	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2255070	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2393669	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2393670	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35355150	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736781	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736782	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757151	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4343916	0.80[AMR][1000 genomes]
rs4573	0.82[EUR][1000 genomes]
rs4713006	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713008	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4871	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6456733	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6456734	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6456735	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6903973	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6910899	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6910930	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6913398	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913462	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6913877	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6918360	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6918506	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6918854	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6922824	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6924838	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6924865	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6925047	0.80[AMR][1000 genomes]
rs6925703	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6925783	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6925895	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6926629	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6930120	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6932156	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6932865	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6933176	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6940053	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6940188	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6941022	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs767471	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9295694	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295695	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295698	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9357010	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9358952	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9358954	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9379887	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9393728	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393729	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9393731	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9393732	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9461259	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9461267	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9461270	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461271	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9461272	0.87[AFR][1000 genomes]
rs9467773	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9467774	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9467775	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467776	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9467778	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467779	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467782	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467783	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467784	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467787	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9467791	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9467796	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9467797	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9467798	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9467799	0.84[AFR][1000 genomes]
rs9467800	0.88[AFR][1000 genomes]
rs9467802	0.87[AFR][1000 genomes]
rs9986382	0.93[AFR][1000 genomes];0.85[EUR][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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28558133	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs28558133	HMGN4	cis	Whole Blood	GTEx
rs28558133	HMGN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26522600-26533200	Weak transcription	NHLF	lung
2	chr6:26522800-26533200	Weak transcription	Ovary	ovary
3	chr6:26523400-26532200	Weak transcription	Primary T cells from cord blood	blood
4	chr6:26523400-26532200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr6:26523400-26533000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:26523400-26533200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:26523600-26533200	Weak transcription	NHDF-Ad	bronchial
8	chr6:26523800-26532200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:26524000-26533200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:26524200-26532400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:26524200-26533200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:26524400-26532200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:26524400-26532400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:26524400-26532600	Weak transcription	A549	lung
15	chr6:26524400-26533000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:26525800-26532800	Weak transcription	Primary B cells from cord blood	blood
17	chr6:26526600-26532200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr6:26526600-26533200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:26528600-26532200	Weak transcription	Fetal Thymus	thymus
20	chr6:26528600-26533200	Weak transcription	Psoas Muscle	Psoas
21	chr6:26528800-26532400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:26528800-26533200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:26529200-26532200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:26529200-26533200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:26529400-26533200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:26529600-26533200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:26529800-26532800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:26529800-26532800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:26529800-26532800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr6:26530000-26533200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr6:26530200-26532200	Weak transcription	K562	blood
32	chr6:26530200-26532800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:26530200-26532800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:26530200-26533000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:26530400-26532200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:26530600-26532400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:26530600-26532600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:26530600-26533200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:26530800-26532600	Weak transcription	Liver	Liver
40	chr6:26531400-26531600	Enhancers	Brain Substantia Nigra	brain
41	chr6:26531400-26532800	Enhancers	Dnd41	blood

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