Variant report

Variant	rs415597
Chromosome Location	chr21:46584782-46584783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46582653..46585265-chr21:46586911..46589357,3	MCF-7	breast:
2	chr21:46574123..46577749-chr21:46583837..46588993,5	K562	blood:
3	chr21:46492545..46495031-chr21:46584204..46586224,2	K562	blood:

Variant related genes	Relation type
ENSG00000268856	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2071873	0.93[ASN][1000 genomes]
rs2838808	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838817	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs373687	0.92[JPT][hapmap]
rs410184	0.82[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers 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
8	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	esv1802303	chr21:46580319-46606676	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs415597	LOC642852	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46557000-46604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr21:46557200-46591800	Weak transcription	HUVEC	blood vessel
3	chr21:46558600-46588800	Weak transcription	Colonic Mucosa	Colon
4	chr21:46560800-46586400	Weak transcription	Liver	Liver
5	chr21:46563000-46595600	Weak transcription	Pancreas	Pancrea
6	chr21:46569000-46587000	Weak transcription	NHEK	skin
7	chr21:46572200-46595600	Weak transcription	Brain Germinal Matrix	brain
8	chr21:46572400-46601000	Weak transcription	Fetal Brain Female	brain
9	chr21:46572800-46604800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr21:46573000-46588400	Weak transcription	Thymus	Thymus
11	chr21:46573600-46591800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr21:46573800-46586800	Weak transcription	Adipose Nuclei	Adipose
13	chr21:46574200-46589200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr21:46575000-46586400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr21:46575000-46587000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr21:46575000-46595600	Weak transcription	Dnd41	blood
17	chr21:46575000-46601000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr21:46575200-46586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr21:46575200-46587000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr21:46575400-46587800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr21:46575400-46588800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr21:46575400-46588800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr21:46575400-46589000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr21:46575400-46604800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr21:46575600-46588800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr21:46576200-46588800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr21:46576200-46595800	Weak transcription	Fetal Lung	lung
28	chr21:46578800-46588800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr21:46579600-46584800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr21:46580400-46591800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr21:46580400-46595600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr21:46581000-46585200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr21:46582000-46585000	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr21:46582000-46590200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr21:46582200-46585200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr21:46582400-46587800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr21:46582400-46589000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr21:46582400-46589400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr21:46582400-46595600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr21:46582400-46595600	Weak transcription	Gastric	stomach
41	chr21:46582600-46585000	Enhancers	Psoas Muscle	Psoas
42	chr21:46582600-46591000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr21:46582600-46598000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr21:46582800-46584800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr21:46582800-46587000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr21:46582800-46592000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr21:46583000-46585200	Enhancers	Fetal Muscle Leg	muscle
48	chr21:46583000-46588800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr21:46583000-46588800	Weak transcription	Hela-S3	cervix
50	chr21:46583200-46584800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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