Variant report

Variant	rs7279563
Chromosome Location	chr21:46294568-46294569
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HMGN3	chr21:46292794-46294626	K562	blood:	n/a	n/a
2	CHD1	chr21:46293902-46294587	GM12878	blood:	n/a	n/a
3	HEY1	chr21:46294341-46294985	HepG2	liver:	n/a	chr21:46294461-46294476
4	POLR2A	chr21:46291742-46295578	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr21:46293221-46294744	K562	blood:	n/a	n/a
6	YY1	chr21:46293901-46294814	GM12878	blood:	n/a	chr21:46294470-46294484
7	E2F6	chr21:46292971-46294673	K562	blood:	n/a	chr21:46294127-46294136 chr21:46293945-46293954 chr21:46294125-46294134 chr21:46293245-46293252 chr21:46293743-46293752
8	POLR2A	chr21:46294438-46294791	GM12891	blood:	n/a	n/a
9	POLR2A	chr21:46291683-46295709	HUVEC	blood vessel:	n/a	n/a
10	STAT5A	chr21:46293886-46295635	GM12878	blood:	n/a	n/a
11	NRF1	chr21:46293360-46294653	SK-N-SH	brain:	n/a	chr21:46294123-46294137 chr21:46293742-46293753 chr21:46293946-46293955 chr21:46293944-46293955 chr21:46293744-46293753 chr21:46293944-46293958 chr21:46293742-46293756 chr21:46293799-46293810 chr21:46293941-46293955 chr21:46293739-46293753
12	POLR2A	chr21:46294295-46295161	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr21:46293394-46295030	HUVEC	blood vessel:	n/a	n/a
14	MAX	chr21:46292245-46294644	K562	blood:	n/a	chr21:46293675-46293685 chr21:46293143-46293152 chr21:46292636-46292646
15	ZBTB33	chr21:46294295-46294660	GM12878	blood:	n/a	n/a
16	MAX	chr21:46293413-46294589	K562	blood:	n/a	chr21:46293675-46293685
17	POLR2A	chr21:46294350-46294941	MCF-7	breast:	n/a	n/a
18	TCF7L2	chr21:46294312-46294833	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr21:46293390-46295090	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr21:46293100-46295496	GM18951	blood:	n/a	n/a
21	RELA	chr21:46293438-46295667	GM18951	blood:	n/a	n/a
22	SIN3AK20	chr21:46294312-46294771	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr21:46293355-46294587	K562	blood:	n/a	n/a
24	POLR2A	chr21:46293191-46295470	GM12892	blood:	n/a	n/a
25	MTA3	chr21:46293899-46295438	GM12878	blood:	n/a	n/a
26	POLR2A	chr21:46294492-46294806	MCF-7	breast:	n/a	n/a
27	POLR2A	chr21:46293358-46295408	GM19193	blood:	n/a	n/a
28	BRCA1	chr21:46294326-46294650	GM12878	blood:	n/a	n/a
29	POLR2A	chr21:46293385-46295571	GM12878	blood:	n/a	n/a
30	POLR2A	chr21:46293349-46295570	GM18526	blood:	n/a	n/a
31	SIN3AK20	chr21:46291542-46294829	MCF-7	breast:	n/a	n/a
32	POLR2A	chr21:46294565-46295257	GM12878	blood:	n/a	n/a
33	MAX	chr21:46293455-46295099	H1-hESC	embryonic stem cell:	n/a	chr21:46293675-46293685
34	MAX	chr21:46293352-46295474	GM12878	blood:	n/a	chr21:46293675-46293685
35	MAX	chr21:46293394-46294829	H1-hESC	embryonic stem cell:	n/a	chr21:46293675-46293685
36	E2F6	chr21:46293389-46294608	K562	blood:	n/a	chr21:46294127-46294136 chr21:46293945-46293954 chr21:46294125-46294134 chr21:46293743-46293752
37	POLR2A	chr21:46293411-46295419	GM12878	blood:	n/a	n/a
38	POLR2A	chr21:46294382-46295055	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr21:46294469-46294801	ProgFib	skin:	n/a	n/a
40	YY1	chr21:46293335-46294631	GM12892	blood:	n/a	chr21:46294470-46294484
41	POLR2A	chr21:46291666-46295051	Hela-S3	cervix:	n/a	n/a
42	BRCA1	chr21:46294289-46294587	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr21:46293391-46294733	K562	blood:	n/a	n/a
44	POLR2A	chr21:46293135-46295590	GM19099	blood:	n/a	n/a
45	EP300	chr21:46294527-46294660	GM12878	blood:	n/a	n/a
46	RCOR1	chr21:46293934-46294704	GM12878	blood:	n/a	n/a
47	POLR2A	chr21:46294445-46294835	Hela-S3	cervix:	n/a	n/a
48	ELF1	chr21:46293928-46294887	K562	blood:	n/a	n/a
49	POLR2A	chr21:46293236-46294885	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr21:46294389-46294904	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:46231216..46239677-chr21:46289090..46295542,14	K562	blood:
2	chr21:46229150..46231758-chr21:46294546..46297296,2	MCF-7	breast:
3	chr21:46232702..46239829-chr21:46289967..46296620,21	MCF-7	breast:
4	chr21:46288744..46296879-chr21:46346201..46354260,26	MCF-7	breast:
5	chr21:46288400..46294755-chr21:46304910..46312238,10	K562	blood:
6	chr21:46291916..46297365-chr21:46358001..46363812,14	MCF-7	breast:
7	chr21:46220413..46223818-chr21:46291771..46295209,8	K562	blood:
8	chr21:46292072..46295985-chr21:46328607..46334685,5	MCF-7	breast:
9	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
10	chr21:46294020..46295642-chr21:47310587..47313582,2	K562	blood:
11	chr21:46231789..46243695-chr21:46286819..46295664,23	MCF-7	breast:
12	chr21:46235517..46239255-chr21:46289829..46295572,6	K562	blood:
13	chr21:46293215..46295653-chr21:46346335..46349274,2	K562	blood:
14	chr21:46218558..46223428-chr21:46289542..46296056,15	MCF-7	breast:
15	chr21:46294382..46294995-chr21:47312113..47312613,2	Hela-S3	cervix:
16	chr21:46194730..46196311-chr21:46292616..46294794,2	K562	blood:

Variant related genes	Relation type
PTTG1IP	TF binding region
ENSG00000160255	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000183250	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000236519	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1054220	0.81[ASN][1000 genomes]
rs13050333	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13050968	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13052639	0.81[ASN][1000 genomes]
rs13053009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2117340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2117341	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236442	0.81[ASN][1000 genomes]
rs2277811	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282114	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34940823	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35199002	0.81[ASN][1000 genomes]
rs35207173	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35424519	0.81[ASN][1000 genomes]
rs35846107	0.81[ASN][1000 genomes]
rs35871743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3810586	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66467973	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67786546	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73238097	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73239703	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv913964	chr21:46223847-46298869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1058550	chr21:46227163-46317934	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv913968	chr21:46249752-46301008	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1060233	chr21:46254075-46323401	Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv913969	chr21:46279505-46472929	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv544479	chr21:46280467-46323401	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	nsv470907	chr21:46283669-46306161	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv459299	chr21:46283669-46311264	Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
15	nsv459300	chr21:46283669-46311264	Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	nsv587814	chr21:46283669-46311264	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	esv3409023	chr21:46292349-46295097	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7279563	PTTG1IP	Cis_1M	lymphoblastoid	RTeQTL
rs7279563	PTTG1IP	cis	lung	GTEx
rs7279563	PTTG1IP	cis	Artery Aorta	GTEx
rs7279563	PTTG1IP	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46289800-46296000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr21:46291200-46295200	Active TSS	Aorta	Aorta
3	chr21:46291800-46295400	Active TSS	Psoas Muscle	Psoas
4	chr21:46292000-46295000	Active TSS	Ovary	ovary
5	chr21:46292000-46295200	Active TSS	Lung	lung
6	chr21:46292200-46294600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr21:46292200-46295200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr21:46292200-46295200	Active TSS	Left Ventricle	heart
9	chr21:46292200-46295400	Active TSS	Right Atrium	heart
10	chr21:46292400-46294600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr21:46292400-46294600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr21:46292400-46294600	Active TSS	Stomach Mucosa	stomach
13	chr21:46292400-46294800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr21:46292400-46294800	Active TSS	Colon Smooth Muscle	Colon
15	chr21:46292400-46294800	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr21:46292400-46294800	Active TSS	Fetal Kidney	kidney
17	chr21:46292400-46294800	Active TSS	Sigmoid Colon	Sigmoid Colon
18	chr21:46292400-46294800	Active TSS	HSMMtube	muscle
19	chr21:46292600-46294600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr21:46292600-46294600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr21:46292600-46294600	Active TSS	GM12878-XiMat	blood
22	chr21:46292600-46294800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr21:46292600-46294800	Active TSS	Brain Cingulate Gyrus	brain
24	chr21:46292600-46294800	Active TSS	Gastric	stomach
25	chr21:46292600-46294800	Active TSS	Placenta Amnion	Placenta Amnion
26	chr21:46292600-46295000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr21:46292600-46295000	Active TSS	Brain Substantia Nigra	brain
28	chr21:46292600-46295000	Active TSS	Esophagus	oesophagus
29	chr21:46292600-46295000	Active TSS	Rectal Smooth Muscle	rectum
30	chr21:46292600-46295200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr21:46292600-46295200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr21:46292600-46295400	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr21:46292800-46294800	Active TSS	Brain Angular Gyrus	brain
34	chr21:46292800-46294800	Active TSS	Brain Anterior Caudate	brain
35	chr21:46292800-46294800	Active TSS	Colonic Mucosa	Colon
36	chr21:46292800-46295000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr21:46292800-46295000	Active TSS	Brain Hippocampus Middle	brain
38	chr21:46292800-46295200	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr21:46292800-46295200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr21:46292800-46295200	Active TSS	Pancreas	Pancrea
41	chr21:46292800-46295400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr21:46292800-46295400	Active TSS	Right Ventricle	heart
43	chr21:46293000-46294600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr21:46293000-46294600	Active TSS	Stomach Smooth Muscle	stomach
45	chr21:46293000-46294800	Active TSS	Spleen	Spleen
46	chr21:46293400-46294600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
47	chr21:46293800-46295400	Flanking Active TSS	HMEC	breast
48	chr21:46294000-46295000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr21:46294000-46295000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
50	chr21:46294000-46295000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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