Variant report

Variant	rs1474490
Chromosome Location	chr21:40716136-40716137
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
2	21:40712819-40717370..21:40748850-40752541	GM12878	blood:
3	chr21:40555173..40557304-chr21:40714737..40716613,2	K562	blood:
4	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:

Variant related genes	Relation type
ENSG00000183527	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1029004	0.84[AMR][1000 genomes]
rs11088470	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11701805	0.83[AMR][1000 genomes]
rs11702505	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11911087	0.82[EUR][1000 genomes]
rs12483559	0.83[EUR][1000 genomes]
rs13047518	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13049907	0.82[EUR][1000 genomes]
rs2056844	0.83[EUR][1000 genomes]
rs2070865	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836952	0.81[AMR][1000 genomes]
rs2836980	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836983	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836984	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2836985	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34890172	0.88[EUR][1000 genomes]
rs35769610	0.83[EUR][1000 genomes]
rs35994303	0.83[EUR][1000 genomes]
rs4818018	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4818019	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59916147	0.80[EUR][1000 genomes]
rs62223011	0.80[EUR][1000 genomes]
rs62223039	0.83[EUR][1000 genomes]
rs62223052	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7282582	0.82[AMR][1000 genomes]
rs8129595	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8133928	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription 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	53 gene(s)	inside rSNPs	diseases
2	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv587483	chr21:40686327-40718161	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv979537	chr21:40714343-40716638	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1474490	PSMG1	cis	Artery Tibial	GTEx
rs1474490	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs1474490	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs1474490	HMGN1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40692400-40718400	Weak transcription	Right Atrium	heart
2	chr21:40704000-40719600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr21:40704600-40717200	Weak transcription	Right Ventricle	heart
4	chr21:40704600-40719600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:40711800-40719600	Weak transcription	Pancreas	Pancrea
6	chr21:40712000-40717200	Strong transcription	Fetal Stomach	stomach
7	chr21:40712200-40716200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr21:40712200-40718800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr21:40712600-40716400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr21:40712600-40716600	Strong transcription	Fetal Brain Female	brain
11	chr21:40712600-40716800	Strong transcription	Dnd41	blood
12	chr21:40712600-40717000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr21:40712600-40717000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr21:40712600-40717000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr21:40712600-40717000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr21:40712600-40717000	Strong transcription	Duodenum Mucosa	Duodenum
17	chr21:40712600-40717200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr21:40712600-40717400	Strong transcription	Fetal Intestine Large	intestine
19	chr21:40712600-40717400	Strong transcription	Fetal Thymus	thymus
20	chr21:40712600-40717400	Strong transcription	Osteobl	bone
21	chr21:40712600-40717600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr21:40712600-40717600	Strong transcription	Fetal Muscle Leg	muscle
23	chr21:40712600-40717600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr21:40712600-40717600	Strong transcription	Thymus	Thymus
25	chr21:40712600-40718200	Strong transcription	HSMM	muscle
26	chr21:40712800-40716200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr21:40712800-40716400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr21:40712800-40716400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr21:40712800-40716400	Strong transcription	Left Ventricle	heart
30	chr21:40712800-40716400	Strong transcription	NH-A	brain
31	chr21:40712800-40716600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr21:40712800-40717000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr21:40712800-40717000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr21:40712800-40717000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr21:40712800-40717000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr21:40712800-40717000	Strong transcription	Fetal Kidney	kidney
37	chr21:40712800-40717000	Strong transcription	HMEC	breast
38	chr21:40712800-40717200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr21:40712800-40717200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr21:40712800-40717400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr21:40712800-40717400	Strong transcription	Liver	Liver
42	chr21:40712800-40717600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr21:40712800-40717600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr21:40712800-40717600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr21:40712800-40717600	Strong transcription	A549	lung
46	chr21:40712800-40717800	Strong transcription	Primary B cells from cord blood	blood
47	chr21:40712800-40717800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr21:40712800-40718400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr21:40712800-40718600	Strong transcription	Primary B cells from peripheral blood	blood
50	chr21:40712800-40719200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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