Variant report

Variant	rs1321480
Chromosome Location	chr6:26532742-26532743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26311628..26314659-chr6:26531812..26534780,3	K562	blood:
2	chr6:26421115..26423072-chr6:26532607..26534934,2	K562	blood:
3	chr6:26530786..26533089-chr6:26568633..26571101,2	K562	blood:
4	chr6:26532421..26535211-chr6:26570479..26571983,2	MCF-7	breast:
5	chr6:26526578..26530250-chr6:26530283..26533379,3	MCF-7	breast:
6	chr6:26531816..26533494-chr6:27804516..27806493,2	K562	blood:
7	chr6:26521199..26522704-chr6:26531334..26533280,2	MCF-7	breast:
8	chr6:26378690..26380275-chr6:26532676..26534577,2	K562	blood:
9	chr6:26526060..26529298-chr6:26530268..26533280,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124549	Chromatin interaction
ENSG00000261353	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000184348	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1001687	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10214634	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10223789	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10223792	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10484442	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1056347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056667	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056668	0.93[EUR][1000 genomes]
rs1078679	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10946834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946837	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11752946	0.83[EUR][1000 genomes]
rs11754138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526680	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12663883	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12663894	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12665431	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1321479	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1321481	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1321482	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1535274	0.81[AMR][1000 genomes]
rs1535276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535277	0.87[AFR][1000 genomes]
rs1570059	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1570060	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1570061	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1884946	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1884947	0.84[EUR][1000 genomes]
rs1884948	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1884949	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1977201	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2024970	0.83[EUR][1000 genomes]
rs2208331	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2224380	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2255070	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2393669	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2393670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28558133	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35355150	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3736781	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736782	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3757151	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4343916	0.81[AMR][1000 genomes]
rs4368798	0.80[AFR][1000 genomes]
rs4573	0.86[EUR][1000 genomes]
rs4713006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713008	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4871	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55930917	0.84[EUR][1000 genomes]
rs6456733	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6456734	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6456735	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6903973	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6909277	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6910899	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913398	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6913462	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6913877	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6918360	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6918506	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6918854	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6922824	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6924838	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6924865	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6925047	0.81[AMR][1000 genomes]
rs6925703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925783	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6925895	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6926629	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6930120	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6932156	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6932350	0.82[EUR][1000 genomes]
rs6932865	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6933176	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6940053	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6940188	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6941022	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs767471	0.96[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9295694	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295698	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9357010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358952	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9358954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379887	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393728	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9393729	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9461259	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9461267	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461270	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9461271	0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9461272	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9461275	0.80[AFR][1000 genomes]
rs9467773	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9467774	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467775	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467776	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9467778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467779	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467782	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467783	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467784	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9467787	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9467791	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9467796	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9467797	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9467798	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9467799	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9467800	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9467802	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9467805	0.81[AFR][1000 genomes]
rs9986382	0.96[AFR][1000 genomes];0.90[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1321480	HMGN4	Cis_1M	lymphoblastoid	RTeQTL
rs1321480	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs1321480	ZNF322	cis	Nerve Tibial	GTEx
rs1321480	HMGN4	cis	Whole Blood	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

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	chr6:26523400-26533000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:26523400-26533200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:26523600-26533200	Weak transcription	NHDF-Ad	bronchial
6	chr6:26524000-26533200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:26524200-26533200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:26524400-26533000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:26525800-26532800	Weak transcription	Primary B cells from cord blood	blood
10	chr6:26526600-26533200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:26528600-26533200	Weak transcription	Psoas Muscle	Psoas
12	chr6:26528800-26533200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:26529200-26533200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:26529400-26533200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:26529600-26533200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:26529800-26532800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:26529800-26532800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:26529800-26532800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:26530000-26533200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:26530200-26532800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:26530200-26532800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:26530200-26533000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:26530600-26533200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:26531400-26532800	Enhancers	Dnd41	blood
25	chr6:26531600-26532800	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr6:26532200-26532800	Enhancers	Fetal Brain Female	brain
27	chr6:26532200-26532800	Enhancers	Fetal Thymus	thymus
28	chr6:26532200-26532800	Enhancers	GM12878-XiMat	blood
29	chr6:26532200-26533000	Enhancers	Primary T cells from cord blood	blood
30	chr6:26532200-26533000	Enhancers	Primary T cells fromperipheralblood	blood
31	chr6:26532200-26533000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:26532200-26533000	Flanking Active TSS	K562	blood
33	chr6:26532200-26533200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr6:26532200-26533200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:26532400-26532800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:26532400-26532800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:26532400-26533000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr6:26532400-26533000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:26532400-26533000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr6:26532400-26533000	Enhancers	Brain Angular Gyrus	brain
41	chr6:26532400-26533000	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr6:26532400-26533000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:26532400-26533200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr6:26532400-26533200	Enhancers	Primary B cells from peripheral blood	blood
45	chr6:26532400-26533200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr6:26532400-26533200	Weak transcription	Brain Substantia Nigra	brain
47	chr6:26532400-26534000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:26532400-26534000	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr6:26532400-26534000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:26532600-26532800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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