Variant report

Variant	rs13050333
Chromosome Location	chr21:46287705-46287706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:46287563-46287735	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr21:46249596..46252365-chr21:46286693..46288889,2	K562	blood:
2	chr21:46272684..46279612-chr21:46286573..46290125,9	K562	blood:
3	chr21:46234824..46239565-chr21:46284858..46289652,5	K562	blood:
4	chr21:46247392..46250185-chr21:46286804..46289409,3	MCF-7	breast:
5	chr21:46217105..46224485-chr21:46287607..46297526,26	MCF-7	breast:
6	chr21:46231789..46243695-chr21:46286819..46295664,23	MCF-7	breast:
7	chr21:46279667..46283456-chr21:46286447..46289465,4	K562	blood:
8	chr21:46286677..46288930-chr6:170126669..170128404,2	K562	blood:
9	chr21:46222162..46224765-chr21:46287052..46289071,2	K562	blood:
10	chr21:46237355..46239033-chr21:46286989..46289637,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGB2-1	chr21:46286389-46288992	ENSG00000250713

No data

Variant related genes	Relation type
PTTG1IP	TF binding region
ENSG00000183255	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000236519	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs13050968	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13053009	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs182893	1.00[JPT][hapmap]
rs2117340	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2117341	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235259	1.00[JPT][hapmap]
rs235284	1.00[JPT][hapmap]
rs2838711	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2838712	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2838713	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2838715	1.00[JPT][hapmap]
rs2838717	1.00[JPT][hapmap]
rs2838718	1.00[JPT][hapmap]
rs34940823	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35207173	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35871743	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3810586	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66467973	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67786546	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7279563	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238097	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73239703	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13050333	PTTG1IP	cis	Artery Aorta	GTEx
rs13050333	PTTG1IP	Cis_1M	lymphoblastoid	RTeQTL
rs13050333	PTTG1IP	cis	Heart Left Ventricle	GTEx
rs13050333	PTTG1IP	cis	Artery Tibial	GTEx
rs13050333	PTTG1IP	cis	lung	GTEx
rs13050333	PTTG1IP	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46275600-46290600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr21:46278400-46289600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr21:46279400-46288400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr21:46279600-46288800	Weak transcription	Fetal Kidney	kidney
5	chr21:46283400-46288800	Strong transcription	NHEK	skin
6	chr21:46284000-46288400	Genic enhancers	Spleen	Spleen
7	chr21:46284000-46289000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr21:46284600-46287800	Genic enhancers	Gastric	stomach
9	chr21:46284800-46288600	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr21:46285000-46288400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr21:46285000-46291600	Enhancers	Primary hematopoietic stem cells	blood
12	chr21:46285000-46291800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr21:46285200-46287800	Genic enhancers	Fetal Intestine Small	intestine
14	chr21:46285200-46287800	Genic enhancers	Stomach Smooth Muscle	stomach
15	chr21:46285200-46287800	Genic enhancers	Dnd41	blood
16	chr21:46285200-46287800	Genic enhancers	NHLF	lung
17	chr21:46285200-46288600	Genic enhancers	Right Ventricle	heart
18	chr21:46285200-46288800	Genic enhancers	Osteobl	bone
19	chr21:46285200-46289000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr21:46285200-46289200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr21:46285200-46290000	Genic enhancers	Fetal Thymus	thymus
22	chr21:46285200-46290800	Enhancers	Right Atrium	heart
23	chr21:46285200-46291600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr21:46285400-46288600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr21:46285400-46289000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr21:46285400-46291600	Enhancers	Left Ventricle	heart
27	chr21:46285600-46288600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr21:46285600-46289400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr21:46285600-46291600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr21:46285600-46291800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr21:46285600-46292200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr21:46285800-46288000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr21:46285800-46288400	Genic enhancers	Fetal Muscle Leg	muscle
34	chr21:46285800-46289000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr21:46285800-46289200	Enhancers	Brain Angular Gyrus	brain
36	chr21:46285800-46289400	Enhancers	Brain Substantia Nigra	brain
37	chr21:46285800-46290000	Enhancers	Brain Anterior Caudate	brain
38	chr21:46286000-46287800	Genic enhancers	Primary T cells from cord blood	blood
39	chr21:46286000-46288000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr21:46286000-46288000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr21:46286000-46289000	Genic enhancers	K562	blood
42	chr21:46286000-46289600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr21:46286000-46289600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr21:46286000-46289600	Enhancers	Colon Smooth Muscle	Colon
45	chr21:46286000-46290600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr21:46286000-46290800	Enhancers	Brain Hippocampus Middle	brain
47	chr21:46286000-46291200	Enhancers	Stomach Mucosa	stomach
48	chr21:46286000-46291600	Enhancers	Liver	Liver
49	chr21:46286200-46287800	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr21:46286200-46288000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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