Variant report

Variant	rs1543423
Chromosome Location	chr20:1451628-1451629
allele	C/T
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	RCOR1	chr20:1450181-1452208	IMR90	lung:	n/a	n/a
2	CTCF	chr20:1451480-1451630	AG10803	skin:	n/a	n/a
3	CHD1	chr20:1450304-1451859	IMR90	lung:	n/a	n/a
4	STAT3	chr20:1451531-1451731	MCF10A-Er-Src	breast:	n/a	n/a
5	MXI1	chr20:1450185-1451990	IMR90	lung:	n/a	n/a
6	CTCF	chr20:1449985-1451820	A549	lung:	n/a	chr20:1450872-1450885 chr20:1450389-1450402 chr20:1450865-1450886 chr20:1450871-1450887 chr20:1450870-1450888
7	POLR2A	chr20:1451553-1451685	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:1447071..1448806-chr20:1450889..1452867,2	MCF-7	breast:
2	chr20:1450041..1452334-chr20:1456617..1458188,2	K562	blood:
3	chr20:1205294..1207984-chr20:1450527..1452708,2	MCF-7	breast:
4	chr20:1397834..1399758-chr20:1450418..1453215,2	K562	blood:

Variant related genes	Relation type
NSFL1C	TF binding region
ENSG00000244588	Chromatin interaction
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1884387	0.97[ASN][1000 genomes]
rs2143832	0.82[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2873565	0.98[ASN][1000 genomes]
rs3795134	0.90[JPT][hapmap]
rs3795135	0.85[JPT][hapmap]
rs6033860	0.88[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6033867	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033871	0.81[LWK][hapmap]
rs6033901	0.88[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6033910	0.92[ASN][1000 genomes]
rs6033950	0.83[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6042462	0.84[GIH][hapmap];0.90[JPT][hapmap]
rs6042499	0.98[ASN][1000 genomes]
rs6042500	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042592	0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6042602	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs6042611	0.90[ASN][1000 genomes]
rs6042650	0.87[ASN][1000 genomes]
rs6042667	0.84[CHD][hapmap]
rs6074680	0.80[ASN][1000 genomes]
rs6074709	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6074715	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6074718	0.83[ASN][1000 genomes]
rs6079277	0.98[ASN][1000 genomes]
rs6079288	0.97[ASN][1000 genomes]
rs6079289	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079294	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6079302	0.97[ASN][1000 genomes]
rs6079317	0.87[ASN][1000 genomes]
rs6079325	0.88[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap]
rs6079330	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6079336	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6079354	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6079361	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6079362	0.91[ASN][1000 genomes]
rs6079376	0.91[ASN][1000 genomes]
rs6105233	0.91[ASN][1000 genomes]
rs6105234	0.91[ASN][1000 genomes]
rs6105240	0.83[ASN][1000 genomes]
rs6110169	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6110207	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6110215	0.91[ASN][1000 genomes]
rs6110226	0.83[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6110228	0.87[ASN][1000 genomes]
rs6110253	0.83[ASN][1000 genomes]
rs6131543	0.98[ASN][1000 genomes]
rs6131553	0.96[ASN][1000 genomes]
rs6131559	0.90[ASN][1000 genomes]
rs6135033	0.90[JPT][hapmap]
rs6135048	0.98[ASN][1000 genomes]
rs6135050	0.98[ASN][1000 genomes]
rs6135060	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6135061	0.83[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6135062	0.96[ASN][1000 genomes]
rs6135063	0.95[ASN][1000 genomes]
rs6135064	0.94[ASN][1000 genomes]
rs6135068	0.95[ASN][1000 genomes]
rs6135069	0.95[ASN][1000 genomes]
rs6135080	0.95[ASN][1000 genomes]
rs6135089	0.83[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6135095	0.83[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6135105	0.91[ASN][1000 genomes]
rs7270432	0.83[ASN][1000 genomes]
rs963867	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1543423	SIRPB2	cis	Whole Blood	GTEx
rs1543423	NSFL1C	cis	Whole Blood	GTEx
rs1543423	PSMF1	cis	cerebellum	SCAN
rs1543423	RP4-776F14.3	cis	Whole Blood	GTEx
rs1543423	NSFL1C	cis	cerebellum	SCAN
rs1543423	SPEF1	cis	parietal	SCAN
rs1543423	NSFL1C	cis	multi-tissue	Pritchard
rs1543423	NSFL1C	cis	lymphoblastoid	seeQTL
rs1543423	EBF4	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1448200-1452200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr20:1448200-1455800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr20:1448200-1457400	Weak transcription	Spleen	Spleen
4	chr20:1448200-1459000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr20:1448400-1452200	Weak transcription	Esophagus	oesophagus
6	chr20:1448800-1452000	Enhancers	Duodenum Mucosa	Duodenum
7	chr20:1448800-1452000	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr20:1449000-1453600	Enhancers	Primary B cells from cord blood	blood
9	chr20:1449000-1454800	Enhancers	Fetal Intestine Small	intestine
10	chr20:1449400-1454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr20:1449400-1454200	Enhancers	K562	blood
12	chr20:1449600-1451800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:1449600-1451800	Enhancers	HMEC	breast
14	chr20:1449600-1452000	Enhancers	HUVEC	blood vessel
15	chr20:1449600-1452800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr20:1449800-1452000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr20:1449800-1453800	Genic enhancers	Monocytes-CD14+_RO01746	blood
18	chr20:1450000-1451800	Enhancers	Hela-S3	cervix
19	chr20:1450000-1453000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
20	chr20:1450200-1451800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr20:1450200-1452000	Enhancers	NHEK	skin
22	chr20:1450400-1453800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr20:1450400-1459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr20:1450400-1459000	Weak transcription	Lung	lung
25	chr20:1450600-1451800	Enhancers	HSMM	muscle
26	chr20:1450600-1452000	Enhancers	Osteobl	bone
27	chr20:1450600-1454600	Weak transcription	Right Ventricle	heart
28	chr20:1450800-1453000	Weak transcription	Fetal Heart	heart
29	chr20:1450800-1454000	Weak transcription	Adipose Nuclei	Adipose
30	chr20:1450800-1456200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr20:1450800-1458200	Genic enhancers	Primary monocytes fromperipheralblood	blood
32	chr20:1451000-1452000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr20:1451000-1452000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr20:1451000-1452600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr20:1451000-1454000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr20:1451200-1451800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr20:1451200-1451800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr20:1451200-1452200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr20:1451200-1452800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr20:1451200-1453800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr20:1451200-1454800	Enhancers	Fetal Intestine Large	intestine
42	chr20:1451200-1456000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr20:1451400-1451800	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr20:1451400-1451800	Enhancers	HSMMtube	muscle
45	chr20:1451400-1451800	Flanking Active TSS	NH-A	brain
46	chr20:1451400-1452000	Bivalent Enhancer	HepG2	liver
47	chr20:1451400-1453000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr20:1451400-1453600	Weak transcription	GM12878-XiMat	blood
49	chr20:1451600-1451800	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr20:1451600-1451800	Flanking Active TSS	A549	lung

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