Variant report

Variant	rs5019244
Chromosome Location	chr20:1402161-1402162
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	chr20:1388186..1390453-chr20:1399929..1402694,2	K562	blood:
2	chr20:1397101..1400734-chr20:1402092..1406050,4	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1028508	0.80[ASN][1000 genomes]
rs11087052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs1884388	0.86[ASN][1000 genomes]
rs1884389	0.81[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1884391	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs1998007	0.85[ASN][1000 genomes]
rs2144542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144545	0.87[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2207829	0.85[ASN][1000 genomes]
rs2207830	0.97[ASN][1000 genomes]
rs2317652	0.80[ASN][1000 genomes]
rs3088080	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs3171292	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs3210915	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs36018423	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4352285	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs4546067	0.84[JPT][hapmap]
rs4813133	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs4814229	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4814231	0.85[ASN][1000 genomes]
rs4814237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814243	0.85[CHB][hapmap];0.81[CHD][hapmap];0.88[ASN][1000 genomes]
rs4814244	0.92[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6033691	0.85[ASN][1000 genomes]
rs6033697	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033698	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033707	0.85[ASN][1000 genomes]
rs6033709	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033710	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033726	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033753	0.89[ASN][1000 genomes]
rs6033807	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs6042066	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042071	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042072	0.85[ASN][1000 genomes]
rs6042074	0.85[ASN][1000 genomes]
rs6042088	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042091	0.85[ASN][1000 genomes]
rs6042117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042175	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042197	0.84[ASN][1000 genomes]
rs6042207	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042208	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042209	0.84[ASN][1000 genomes]
rs6042238	0.80[ASN][1000 genomes]
rs6042244	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs6042270	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6042283	0.80[ASN][1000 genomes]
rs6042292	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs6042354	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs6074593	0.85[ASN][1000 genomes]
rs6074623	0.93[ASN][1000 genomes]
rs6079009	0.85[ASN][1000 genomes]
rs6079010	0.85[ASN][1000 genomes]
rs6079012	0.85[ASN][1000 genomes]
rs6079013	0.85[ASN][1000 genomes]
rs6079015	0.85[ASN][1000 genomes]
rs6079133	0.88[JPT][hapmap]
rs6105079	0.85[ASN][1000 genomes]
rs6105081	0.85[ASN][1000 genomes]
rs6105102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105110	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs6105165	0.89[JPT][hapmap]
rs6109825	0.85[ASN][1000 genomes]
rs6109893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109894	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131468	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6134916	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6514382	0.85[ASN][1000 genomes]
rs6514383	0.85[ASN][1000 genomes]
rs6891	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs750424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124053	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs873523	0.84[ASN][1000 genomes]
rs910619	0.87[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs910620	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs926977	0.89[ASN][1000 genomes]
rs932524	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs9575	0.89[JPT][hapmap]

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	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs5019244	NSFL1C	cis	brain	seeQTL
rs5019244	NSFL1C	cis	Brain Pons	GTEx
rs5019244	NSFL1C	cis	Frontal Cortex	GTEx
rs5019244	NSFL1C	cis	Temporal Cortex	GTEx
rs5019244	NSFL1C	cis	cerebellum	SCAN
rs5019244	CENPB	cis	cerebellum	SCAN
rs5019244	DEFB125	cis	cerebellum	SCAN
rs5019244	NSFL1C	cis	lymphoblastoid	seeQTL
rs5019244	NSFL1C	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1399400-1403200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:1399800-1404400	Weak transcription	NHLF	lung
3	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr20:1400000-1403200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:1400000-1404200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr20:1400000-1408200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr20:1400000-1410600	Weak transcription	Osteobl	bone
8	chr20:1400600-1403600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:1401600-1402600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr20:1401800-1404400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:1401800-1404600	Enhancers	Placenta	Placenta

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