Variant report

Variant	rs2117341
Chromosome Location	chr21:46302393-46302394
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46299899..46304790-chr21:46308846..46313230,4	K562	blood:
2	chr21:46296431..46298855-chr21:46300114..46303046,3	K562	blood:
3	chr21:46220171..46223743-chr21:46298474..46302902,5	MCF-7	breast:
4	chr21:46296431..46298316-chr21:46299911..46303046,4	K562	blood:
5	chr21:46300926..46303863-chr21:46305072..46307882,3	K562	blood:
6	chr21:46292064..46297590-chr21:46299437..46304733,9	MCF-7	breast:
7	chr21:46300718..46303390-chr21:46325614..46327160,2	MCF-7	breast:
8	chr21:46302013..46304883-chr21:46310101..46313045,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184787	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000160255	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1054220	0.81[ASN][1000 genomes]
rs13050333	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13050968	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13052639	0.81[ASN][1000 genomes]
rs13053009	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2117340	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236442	0.81[ASN][1000 genomes]
rs2277811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282114	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs235259	0.82[CHB][hapmap]
rs235340	0.82[CHB][hapmap]
rs2838711	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs2838712	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs2838713	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs34940823	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35199002	0.81[ASN][1000 genomes]
rs35207173	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[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3810586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66467973	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67786546	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7279563	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238097	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73239703	0.98[EUR][1000 genomes];0.97[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	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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv470908	chr21:46298869-46335580	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2117341	PTTG1IP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46295200-46302600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr21:46295200-46304200	Weak transcription	Esophagus	oesophagus
3	chr21:46295600-46338800	Weak transcription	Right Atrium	heart
4	chr21:46295800-46303600	Enhancers	Primary B cells from cord blood	blood
5	chr21:46296000-46303800	Enhancers	Primary hematopoietic stem cells	blood
6	chr21:46296000-46304600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr21:46296000-46307400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr21:46297800-46302600	Enhancers	HUVEC	blood vessel
9	chr21:46297800-46302800	Enhancers	Primary B cells from peripheral blood	blood
10	chr21:46298200-46304200	Enhancers	Spleen	Spleen
11	chr21:46298400-46326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr21:46299600-46302600	Enhancers	Primary T cells from cord blood	blood
13	chr21:46299800-46302800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr21:46299800-46302800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr21:46299800-46303000	Enhancers	Fetal Thymus	thymus
16	chr21:46299800-46303400	Enhancers	HSMMtube	muscle
17	chr21:46300000-46302400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr21:46300000-46302800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr21:46300000-46302800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr21:46300000-46302800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr21:46300000-46303000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr21:46300000-46303400	Enhancers	HSMM	muscle
23	chr21:46300000-46304200	Enhancers	Placenta	Placenta
24	chr21:46300200-46302400	Enhancers	Primary T cells fromperipheralblood	blood
25	chr21:46300200-46302400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr21:46300200-46302400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr21:46300200-46302800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr21:46300200-46303600	Enhancers	Adipose Nuclei	Adipose
29	chr21:46300200-46303800	Enhancers	HMEC	breast
30	chr21:46300200-46304600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr21:46300400-46302600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr21:46300400-46302800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr21:46300400-46303000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr21:46300400-46303000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr21:46300400-46310000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr21:46300600-46302400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr21:46300600-46302800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr21:46300600-46303200	Enhancers	NHEK	skin
39	chr21:46300600-46303600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr21:46300800-46302400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr21:46300800-46302600	Enhancers	NHDF-Ad	bronchial
42	chr21:46301000-46302400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr21:46301000-46302800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr21:46301000-46303000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr21:46301000-46303200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr21:46301000-46303600	Enhancers	Fetal Intestine Large	intestine
47	chr21:46301000-46303600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr21:46301200-46302600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr21:46301200-46302600	Enhancers	GM12878-XiMat	blood
50	chr21:46301200-46302800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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