Variant report

Variant	rs55836299
Chromosome Location	chr21:40651426-40651427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40650313..40652723-chr21:40719146..40721312,2	MCF-7	breast:
2	chr21:40650245..40652067-chr21:40661600..40663535,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205581	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1041440	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10427502	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1065242	0.86[AMR][1000 genomes]
rs11910151	0.82[AMR][1000 genomes]
rs12151994	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12481860	0.86[AMR][1000 genomes]
rs12482181	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12483216	0.86[AMR][1000 genomes]
rs12710453	0.90[EUR][1000 genomes]
rs12710454	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13047663	0.81[EUR][1000 genomes]
rs13048178	0.84[AMR][1000 genomes]
rs13049280	0.89[EUR][1000 genomes]
rs13052882	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13339986	0.90[EUR][1000 genomes]
rs13625	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs14194	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1541102	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1571709	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1984022	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2026265	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2026267	0.86[AMR][1000 genomes]
rs2150415	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2234543	0.84[AMR][1000 genomes]
rs2735306	0.86[AMR][1000 genomes]
rs2735309	0.86[AMR][1000 genomes]
rs2776307	0.86[AMR][1000 genomes]
rs2776308	0.86[AMR][1000 genomes]
rs2776309	0.86[AMR][1000 genomes]
rs28360661	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836923	0.82[AMR][1000 genomes]
rs2836925	0.86[AMR][1000 genomes]
rs2836927	0.86[AMR][1000 genomes]
rs2836929	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836932	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836933	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2836938	0.87[AMR][1000 genomes]
rs2836944	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836953	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836955	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836957	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836964	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836965	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2836967	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2836968	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836972	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2836973	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2836974	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2836977	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34035316	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34176878	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34294410	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34394827	0.80[AMR][1000 genomes]
rs34433511	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34578707	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34672724	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34978594	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35068861	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35123057	0.86[AMR][1000 genomes]
rs35386515	0.84[AMR][1000 genomes]
rs35560196	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35571600	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35774464	0.83[EUR][1000 genomes]
rs36113648	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3945	0.81[EUR][1000 genomes]
rs56049536	0.84[AMR][1000 genomes]
rs56306759	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6517519	0.86[AMR][1000 genomes]
rs6517521	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6517523	0.86[AMR][1000 genomes]
rs6517526	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6517527	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6517533	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6517538	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66465538	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68004583	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs68090597	0.89[AMR][1000 genomes]
rs71184665	0.80[AMR][1000 genomes]
rs7277978	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7280375	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7282624	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7283420	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7283516	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7283569	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73221174	0.82[AMR][1000 genomes]
rs73221193	0.83[AMR][1000 genomes]
rs7354783	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8127087	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8128026	0.87[AMR][1000 genomes]
rs8128102	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8128620	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8128734	0.84[AMR][1000 genomes]
rs8128827	0.86[AMR][1000 genomes]
rs8128894	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8129147	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8129303	0.86[AMR][1000 genomes]
rs8129355	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8129416	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8130984	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8131965	0.89[AMR][1000 genomes]
rs8133146	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8134733	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9941894	0.83[AMR][1000 genomes];0.94[EUR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs55836299	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs55836299	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs55836299	PSMG1	cis	lung	GTEx
rs55836299	PSMG1	cis	Muscle Skeletal	GTEx
rs55836299	PSMG1	cis	Nerve Tibial	GTEx
rs55836299	PSMG1	cis	Esophagus Mucosa	GTEx
rs55836299	PSMG1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr21:40565400-40653600	Strong transcription	Dnd41	blood
7	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr21:40603200-40653400	Weak transcription	Right Atrium	heart
10	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr21:40613400-40652000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr21:40614000-40654400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr21:40614600-40654200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr21:40614800-40652400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr21:40616400-40651800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr21:40618000-40659200	Weak transcription	Stomach Mucosa	stomach
17	chr21:40619400-40656200	Weak transcription	Ovary	ovary
18	chr21:40619600-40660200	Weak transcription	Brain Angular Gyrus	brain
19	chr21:40625800-40652400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr21:40626200-40653400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr21:40626800-40654000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr21:40630200-40652200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr21:40630200-40661600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr21:40630200-40662800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr21:40630400-40653800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr21:40631200-40663600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr21:40631600-40653400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr21:40631800-40653600	Strong transcription	Fetal Intestine Large	intestine
29	chr21:40633200-40653600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr21:40633200-40662800	Weak transcription	Esophagus	oesophagus
31	chr21:40635800-40653400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr21:40635800-40653600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr21:40636600-40652000	Weak transcription	Fetal Heart	heart
34	chr21:40636600-40659000	Weak transcription	Colon Smooth Muscle	Colon
35	chr21:40638200-40665000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr21:40638600-40657000	Weak transcription	HMEC	breast
37	chr21:40638600-40659800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr21:40638600-40663400	Weak transcription	Gastric	stomach
39	chr21:40638600-40663400	Weak transcription	Psoas Muscle	Psoas
40	chr21:40638600-40665600	Weak transcription	Spleen	Spleen
41	chr21:40639000-40659200	Weak transcription	Brain Substantia Nigra	brain
42	chr21:40639000-40662600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr21:40639000-40663400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr21:40639200-40659600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr21:40641000-40661400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
47	chr21:40642600-40652400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr21:40642600-40653600	Strong transcription	Liver	Liver
49	chr21:40642600-40658800	Weak transcription	A549	lung
50	chr21:40642600-40659200	Weak transcription	HUVEC	blood vessel

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