Variant report

Variant	rs2164072
Chromosome Location	chr21:46301008-46301009
allele	A/C
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:0)
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	chr21:46299899..46304790-chr21:46308846..46313230,4	K562	blood:
2	chr21:46298787..46301754-chr21:46366839..46368624,2	K562	blood:
3	chr21:46296431..46298855-chr21:46300114..46303046,3	K562	blood:
4	chr21:46220171..46223743-chr21:46298474..46302902,5	MCF-7	breast:
5	chr21:46296431..46298316-chr21:46299911..46303046,4	K562	blood:
6	chr21:46292144..46295711-chr21:46299536..46302276,5	K562	blood:
7	chr21:46300926..46303863-chr21:46305072..46307882,3	K562	blood:
8	chr21:46292064..46297590-chr21:46299437..46304733,9	MCF-7	breast:
9	chr21:46220600..46223152-chr21:46298751..46301224,2	K562	blood:
10	chr21:46300718..46303390-chr21:46325614..46327160,2	MCF-7	breast:

No data

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

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1160263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11701641	1.00[ASW][hapmap]
rs11702657	1.00[AFR][1000 genomes]
rs1344110	1.00[ASW][hapmap];0.83[CHB][hapmap];1.00[AFR][1000 genomes]
rs17219671	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1973876	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2248034	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2277810	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2282113	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2282115	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs55927826	1.00[AFR][1000 genomes]
rs60220267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62221469	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62221471	0.93[ASN][1000 genomes]
rs62221472	0.96[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	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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2164072	KRTAP10-9	cis	parietal	SCAN
rs2164072	PTTG1IP	cis	multi-tissue	Pritchard

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46295200-46301200	Weak transcription	Pancreas	Pancrea
2	chr21:46295200-46301400	Weak transcription	Lung	lung
3	chr21:46295200-46302600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:46295200-46304200	Weak transcription	Esophagus	oesophagus
5	chr21:46295600-46338800	Weak transcription	Right Atrium	heart
6	chr21:46295800-46301200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr21:46295800-46301400	Weak transcription	Brain Anterior Caudate	brain
8	chr21:46295800-46303600	Enhancers	Primary B cells from cord blood	blood
9	chr21:46296000-46301600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr21:46296000-46301600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr21:46296000-46303800	Enhancers	Primary hematopoietic stem cells	blood
12	chr21:46296000-46304600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr21:46296000-46307400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr21:46297800-46302600	Enhancers	HUVEC	blood vessel
15	chr21:46297800-46302800	Enhancers	Primary B cells from peripheral blood	blood
16	chr21:46298200-46304200	Enhancers	Spleen	Spleen
17	chr21:46298400-46326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr21:46298800-46301200	Weak transcription	Liver	Liver
19	chr21:46299000-46301400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr21:46299000-46302000	Enhancers	K562	blood
21	chr21:46299400-46301200	Weak transcription	Fetal Intestine Small	intestine
22	chr21:46299600-46302600	Enhancers	Primary T cells from cord blood	blood
23	chr21:46299800-46301200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr21:46299800-46302200	Enhancers	Thymus	Thymus
25	chr21:46299800-46302800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr21:46299800-46302800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr21:46299800-46303000	Enhancers	Fetal Thymus	thymus
28	chr21:46299800-46303400	Enhancers	HSMMtube	muscle
29	chr21:46300000-46302000	Weak transcription	Brain Substantia Nigra	brain
30	chr21:46300000-46302400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr21:46300000-46302800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr21:46300000-46302800	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr21:46300000-46302800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr21:46300000-46303000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr21:46300000-46303400	Enhancers	HSMM	muscle
36	chr21:46300000-46304200	Enhancers	Placenta	Placenta
37	chr21:46300200-46301600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr21:46300200-46301600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr21:46300200-46301600	Enhancers	Hela-S3	cervix
40	chr21:46300200-46302200	Enhancers	NH-A	brain
41	chr21:46300200-46302400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr21:46300200-46302400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr21:46300200-46302400	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr21:46300200-46302800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr21:46300200-46303600	Enhancers	Adipose Nuclei	Adipose
46	chr21:46300200-46303800	Enhancers	HMEC	breast
47	chr21:46300200-46304600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr21:46300400-46301400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr21:46300400-46301400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr21:46300400-46301600	Weak transcription	Brain Hippocampus Middle	brain

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