Variant report

Variant	rs963867
Chromosome Location	chr20:1453039-1453040
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1449411..1451368-chr20:1451842..1453963,2	K562	blood:
2	chr20:1397834..1399758-chr20:1450418..1453215,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1543423	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]
rs1884387	0.97[ASN][1000 genomes]
rs2143832	0.88[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	0.94[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6033867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033871	0.80[YRI][hapmap]
rs6033901	0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6033910	0.92[ASN][1000 genomes]
rs6033950	0.89[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042506	0.91[LWK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs6042544	0.81[CHB][hapmap]
rs6042592	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6042602	1.00[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	0.88[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6074715	0.83[CHB][hapmap];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	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6079302	0.97[ASN][1000 genomes]
rs6079317	0.87[ASN][1000 genomes]
rs6079325	0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap]
rs6079330	0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6079336	0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6079354	0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6079361	0.89[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];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6110207	0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6110215	0.91[ASN][1000 genomes]
rs6110226	0.89[CHB][hapmap];0.97[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	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6135061	0.89[CHB][hapmap];0.97[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	0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6135095	0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6135105	0.91[ASN][1000 genomes]
rs7270432	0.83[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs963867	RP4-776F14.3	cis	Whole Blood	GTEx
rs963867	SPEF1	cis	parietal	SCAN
rs963867	NSFL1C	cis	lymphoblastoid	seeQTL
rs963867	NSFL1C	cis	Whole Blood	GTEx
rs963867	EBF4	cis	cerebellum	SCAN
rs963867	NSFL1C	cis	cerebellum	SCAN
rs963867	NSFL1C	cis	multi-tissue	Pritchard
rs963867	PSMF1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1448200-1455800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:1448200-1457400	Weak transcription	Spleen	Spleen
3	chr20:1448200-1459000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr20:1449000-1453600	Enhancers	Primary B cells from cord blood	blood
5	chr20:1449000-1454800	Enhancers	Fetal Intestine Small	intestine
6	chr20:1449400-1454000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:1449400-1454200	Enhancers	K562	blood
8	chr20:1449800-1453800	Genic enhancers	Monocytes-CD14+_RO01746	blood
9	chr20:1450400-1453800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr20:1450400-1459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:1450400-1459000	Weak transcription	Lung	lung
12	chr20:1450600-1454600	Weak transcription	Right Ventricle	heart
13	chr20:1450800-1454000	Weak transcription	Adipose Nuclei	Adipose
14	chr20:1450800-1456200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr20:1450800-1458200	Genic enhancers	Primary monocytes fromperipheralblood	blood
16	chr20:1451000-1454000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr20:1451200-1453800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr20:1451200-1454800	Enhancers	Fetal Intestine Large	intestine
19	chr20:1451200-1456000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr20:1451400-1453600	Weak transcription	GM12878-XiMat	blood
21	chr20:1451600-1453800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr20:1451600-1454000	Weak transcription	Small Intestine	intestine
23	chr20:1451600-1455600	Weak transcription	Placenta	Placenta
24	chr20:1451600-1459000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:1451800-1455600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr20:1452000-1453200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr20:1452000-1453400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr20:1452000-1454000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr20:1452000-1454000	Weak transcription	A549	lung
30	chr20:1452000-1454000	Weak transcription	Osteobl	bone
31	chr20:1452000-1455200	Weak transcription	NHEK	skin
32	chr20:1452000-1455600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr20:1452000-1459000	Weak transcription	HUVEC	blood vessel
34	chr20:1452000-1459000	Weak transcription	NH-A	brain
35	chr20:1452200-1454200	Enhancers	Primary B cells from peripheral blood	blood
36	chr20:1452200-1454200	Enhancers	Esophagus	oesophagus
37	chr20:1452400-1454600	Enhancers	Duodenum Mucosa	Duodenum
38	chr20:1452400-1454600	Weak transcription	HMEC	breast
39	chr20:1452600-1453200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr20:1452600-1454400	Enhancers	Primary hematopoietic stem cells	blood
41	chr20:1452800-1453800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr20:1452800-1454400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr20:1452800-1454400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr20:1453000-1454200	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr20:1453000-1454400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
46	chr20:1453000-1454400	Enhancers	Stomach Mucosa	stomach

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