Variant report

Variant	rs12482317
Chromosome Location	chr21:40588241-40588242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40588215-40588339	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	21:40583765-40590917..21:40718004-40719183	GM12878	blood:
2	21:40583765-40590917..21:40796857-40798340	Hela-S3	cervix:
3	chr21:40586470..40588300-chr21:40610304..40612724,2	K562	blood:

Variant related genes	Relation type
TIMM9P2	TF binding region
ENSG00000205581	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2836950	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836961	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4818008	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62222988	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62223042	0.91[EUR][1000 genomes]
rs8134638	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056683	chr21:40570023-40673210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12482317	PSMG1	cis	Artery Tibial	GTEx
rs12482317	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs12482317	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs12482317	HMGN1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
3	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40563600-40588600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr21:40565000-40592600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr21:40565400-40653600	Strong transcription	Dnd41	blood
15	chr21:40565600-40590200	Strong transcription	Liver	Liver
16	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr21:40565800-40590600	Strong transcription	Fetal Thymus	thymus
18	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr21:40566200-40590600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr21:40566200-40590600	Strong transcription	Adipose Nuclei	Adipose
21	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr21:40567400-40592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr21:40570600-40589800	Weak transcription	Stomach Mucosa	stomach
25	chr21:40571400-40602400	Weak transcription	Fetal Brain Male	brain
26	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
27	chr21:40573800-40593600	Weak transcription	A549	lung
28	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
29	chr21:40575200-40589400	Weak transcription	NHEK	skin
30	chr21:40576200-40590400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr21:40576200-40597400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr21:40576400-40592400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr21:40576600-40588600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr21:40576600-40589000	Strong transcription	Primary B cells from cord blood	blood
35	chr21:40576800-40589600	Weak transcription	HUVEC	blood vessel
36	chr21:40576800-40593600	Weak transcription	Right Atrium	heart
37	chr21:40577200-40593800	Weak transcription	Colon Smooth Muscle	Colon
38	chr21:40577200-40595400	Weak transcription	Colonic Mucosa	Colon
39	chr21:40577600-40589400	Weak transcription	Brain Hippocampus Middle	brain
40	chr21:40577600-40596000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr21:40577800-40598800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr21:40578000-40589000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr21:40578000-40589600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr21:40578000-40595600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr21:40578000-40598800	Weak transcription	Gastric	stomach
46	chr21:40578000-40607600	Weak transcription	Aorta	Aorta
47	chr21:40578400-40589400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr21:40578600-40588400	Weak transcription	Ovary	ovary
49	chr21:40578600-40595400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr21:40578600-40595400	Weak transcription	Brain Inferior Temporal Lobe	brain

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