Variant report

Variant	rs1054220
Chromosome Location	chr21:46269710-46269711
allele	G/T
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:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46264289..46271339-chr21:46271625..46276632,16	K562	blood:
2	chr21:46267660..46269826-chr21:46493577..46495142,2	K562	blood:
3	chr21:46221083..46222919-chr21:46268127..46270057,2	MCF-7	breast:
4	chr21:46244628..46247469-chr21:46269469..46271474,2	MCF-7	breast:
5	chr21:46264887..46267295-chr21:46268362..46270043,2	K562	blood:
6	chr21:46220705..46222857-chr21:46268688..46270997,2	MCF-7	breast:
7	chr21:46266846..46268611-chr21:46268857..46270465,2	MCF-7	breast:
8	chr21:46269227..46272682-chr21:46358261..46360343,3	K562	blood:
9	chr21:46220969..46223089-chr21:46268593..46270821,2	K562	blood:
10	chr21:46264380..46268999-chr21:46269204..46276124,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM207A-8	chr21:46269504-46270003	NONHSAT082883

No data

Variant related genes	Relation type
ENSG00000183250	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000184787	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13050968	0.81[ASN][1000 genomes]
rs13052639	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2117340	0.81[ASN][1000 genomes]
rs2117341	0.81[ASN][1000 genomes]
rs2236442	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838711	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838712	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838713	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35199002	1.00[ASN][1000 genomes]
rs35424519	1.00[ASN][1000 genomes]
rs35432315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35846107	1.00[ASN][1000 genomes]
rs3810586	0.81[ASN][1000 genomes]
rs7279563	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv459298	chr21:46223847-46277968	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv587813	chr21:46223847-46277968	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv913963	chr21:46223847-46277968	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	nsv913967	chr21:46249752-46279505	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1054220	PTTG1IP	cis	Heart Left Ventricle	GTEx
rs1054220	PTTG1IP	cis	Artery Tibial	GTEx
rs1054220	PTTG1IP	cis	lung	GTEx
rs1054220	PTTG1IP	cis	Artery Aorta	GTEx
rs1054220	PTTG1IP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46266600-46278800	Weak transcription	Fetal Kidney	kidney
2	chr21:46266800-46269800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr21:46266800-46270400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr21:46267200-46274000	Weak transcription	Small Intestine	intestine
5	chr21:46267400-46271600	Genic enhancers	Fetal Intestine Small	intestine
6	chr21:46267400-46285200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr21:46267400-46286600	Strong transcription	Fetal Stomach	stomach
8	chr21:46267600-46270200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr21:46267600-46273000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:46267600-46277000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr21:46267600-46280600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr21:46267600-46287000	Strong transcription	Brain Germinal Matrix	brain
13	chr21:46267800-46273400	Weak transcription	Right Atrium	heart
14	chr21:46267800-46273600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr21:46268000-46273000	Strong transcription	Placenta	Placenta
16	chr21:46268000-46278800	Strong transcription	Stomach Smooth Muscle	stomach
17	chr21:46268000-46281200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr21:46268200-46274000	Strong transcription	Fetal Muscle Trunk	muscle
19	chr21:46268200-46278400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr21:46268200-46281200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr21:46268200-46285800	Strong transcription	Fetal Muscle Leg	muscle
22	chr21:46268600-46270200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr21:46268600-46270200	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr21:46268600-46270400	Strong transcription	Fetal Thymus	thymus
25	chr21:46268600-46270600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr21:46268600-46270600	Genic enhancers	Monocytes-CD14+_RO01746	blood
27	chr21:46268600-46270800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr21:46268600-46271000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr21:46268600-46271200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr21:46268600-46271400	Genic enhancers	Colonic Mucosa	Colon
31	chr21:46268600-46271400	Strong transcription	NHEK	skin
32	chr21:46268600-46271600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr21:46268600-46271600	Strong transcription	Brain Cingulate Gyrus	brain
34	chr21:46268600-46271600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr21:46268600-46272000	Strong transcription	Brain Substantia Nigra	brain
36	chr21:46268600-46272200	Genic enhancers	Duodenum Mucosa	Duodenum
37	chr21:46268600-46272200	Strong transcription	Left Ventricle	heart
38	chr21:46268600-46273400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr21:46268600-46273600	Strong transcription	Spleen	Spleen
40	chr21:46268600-46273800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr21:46268600-46274400	Genic enhancers	Fetal Intestine Large	intestine
42	chr21:46268600-46276600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr21:46268600-46276600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr21:46268600-46277600	Strong transcription	Brain Hippocampus Middle	brain
45	chr21:46268600-46277600	Strong transcription	HMEC	breast
46	chr21:46268600-46278200	Strong transcription	Adipose Nuclei	Adipose
47	chr21:46268600-46278400	Strong transcription	Lung	lung
48	chr21:46268600-46278600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr21:46268600-46279800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr21:46268600-46280600	Strong transcription	H1 Cell Line	embryonic stem cell

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