Variant report

Variant	rs4818019
Chromosome Location	chr21:40694456-40694457
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr21:40693297-40695267	MCF-7	breast:	n/a	n/a
2	EP300	chr21:40693292-40694585	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr21:40693293-40694502	MCF-7	breast:	n/a	n/a
4	NR2F2	chr21:40693294-40695179	MCF-7	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
2	chr21:40691963..40695047-chr21:40751458..40754017,3	MCF-7	breast:
3	chr21:40693407..40696384-chr21:40756189..40758708,3	MCF-7	breast:
4	chr21:40693463..40696053-chr21:40759629..40761307,2	MCF-7	breast:

No data

Variant related genes	Relation type
BRWD1	TF binding region
ENSG00000182093	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000205581	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1029004	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11088466	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11088470	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11701805	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11702505	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11910232	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11911087	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12483559	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12627205	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13047518	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13049907	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1474490	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1980407	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2056844	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2070865	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2150411	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2150413	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2150414	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2297256	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2836926	0.80[EUR][1000 genomes]
rs2836930	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2836931	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2836934	0.82[EUR][1000 genomes]
rs2836940	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836942	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2836943	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836945	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836948	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2836949	0.86[EUR][1000 genomes]
rs2836952	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2836956	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2836958	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2836959	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2836966	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836980	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836983	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836984	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836985	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3171465	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34890172	0.87[EUR][1000 genomes]
rs35769610	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35994303	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4816617	0.80[EUR][1000 genomes]
rs4816618	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4818001	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4818018	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59916147	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62223011	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62223039	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62223052	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7276046	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7278297	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7279497	0.80[EUR][1000 genomes]
rs7282582	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8127379	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8127986	0.81[AFR][1000 genomes]
rs8129595	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8130162	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8130240	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8130320	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8131132	0.80[EUR][1000 genomes]
rs8132143	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8132424	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8133928	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8134214	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8134843	0.80[EUR][1000 genomes]
rs997147	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv587482	chr21:40684427-40706594	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4818019	HMGN1	cis	multi-tissue	Pritchard
rs4818019	PSMG1	cis	Artery Tibial	GTEx
rs4818019	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs4818019	HMGN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40690800-40694600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr21:40692400-40694600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr21:40692400-40718400	Weak transcription	Right Atrium	heart
4	chr21:40693200-40694600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr21:40693200-40694800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr21:40693400-40694600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:40693400-40694600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr21:40693400-40694600	Enhancers	NHDF-Ad	bronchial
9	chr21:40693400-40694600	Enhancers	NHEK	skin
10	chr21:40693400-40694800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr21:40693400-40694800	Enhancers	HepG2	liver
12	chr21:40693400-40695000	Enhancers	Hela-S3	cervix
13	chr21:40693800-40694600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr21:40694000-40694600	Enhancers	A549	lung
15	chr21:40694000-40694800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr21:40694000-40694800	Weak transcription	K562	blood
17	chr21:40694200-40694800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr21:40694200-40695800	Enhancers	Placenta	Placenta
19	chr21:40694400-40694600	Enhancers	Right Ventricle	heart
20	chr21:40694400-40694600	Enhancers	HSMMtube	muscle
21	chr21:40694400-40694800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin

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