Variant report

Variant	rs9575
Chromosome Location	chr20:1426393-1426394
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1426132..1428565-chr20:1431551..1433771,2	K562	blood:
2	chr20:1408801..1411564-chr20:1423013..1426503,3	K562	blood:
3	chr20:1423089..1427509-chr20:1447458..1449907,4	K562	blood:
4	chr20:1425687..1427790-chr20:1442329..1444448,2	K562	blood:
5	chr20:1421730..1423877-chr20:1425978..1428571,2	K562	blood:
6	chr20:1422404..1428420-chr20:1445721..1449907,7	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1028508	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11087052	0.89[JPT][hapmap]
rs11699735	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13063	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs1884388	0.82[ASN][1000 genomes]
rs1884389	0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1884391	0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2144544	0.94[ASN][1000 genomes]
rs2144545	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2144546	0.85[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs2317513	0.92[ASN][1000 genomes]
rs2317651	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2317652	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3088080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3171292	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs3210915	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs3795135	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs3829698	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4352285	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4546067	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4813133	0.84[JPT][hapmap]
rs4814237	0.89[JPT][hapmap]
rs4814240	0.89[JPT][hapmap]
rs4814244	0.84[JPT][hapmap]
rs6033710	0.89[JPT][hapmap]
rs6033715	0.89[JPT][hapmap]
rs6033807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042117	0.89[JPT][hapmap]
rs6042118	0.89[JPT][hapmap]
rs6042238	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042244	0.84[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6042268	0.94[ASN][1000 genomes]
rs6042270	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042283	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042292	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6042354	0.92[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6074631	0.83[ASN][1000 genomes]
rs6079133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079138	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6079139	0.95[ASN][1000 genomes]
rs6105102	0.89[JPT][hapmap]
rs6105110	0.84[JPT][hapmap]
rs6105165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6131506	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6131519	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8124053	0.89[JPT][hapmap]
rs910619	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs910620	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs932524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9575	NSFL1C	cis	Frontal Cortex	GTEx
rs9575	NSFL1C	cis	multi-tissue	Pritchard
rs9575	NSFL1C	cis	Cerebellum	GTEx
rs9575	NSFL1C	cis	Temporal Cortex	GTEx
rs9575	NSFL1C	Cis_1M	lymphoblastoid	RTeQTL
rs9575	NSFL1C	cis	Brain Pons	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
2	chr20:1419000-1430600	Strong transcription	Fetal Stomach	stomach
3	chr20:1419000-1431400	Strong transcription	Brain Germinal Matrix	brain
4	chr20:1419000-1431800	Strong transcription	Brain Hippocampus Middle	brain
5	chr20:1419200-1430200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr20:1419200-1431800	Strong transcription	Stomach Smooth Muscle	stomach
7	chr20:1419200-1443400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr20:1419600-1428800	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr20:1419600-1429200	Strong transcription	Fetal Muscle Leg	muscle
10	chr20:1419600-1431000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr20:1419600-1432000	Strong transcription	Fetal Intestine Large	intestine
12	chr20:1419600-1442000	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr20:1419800-1430000	Strong transcription	Brain Anterior Caudate	brain
14	chr20:1419800-1443600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr20:1420000-1431400	Strong transcription	Fetal Brain Female	brain
16	chr20:1420000-1431600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr20:1420000-1431600	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr20:1420000-1431800	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr20:1420000-1431800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr20:1420000-1432000	Strong transcription	Liver	Liver
21	chr20:1420200-1428800	Strong transcription	Lung	lung
22	chr20:1420200-1430600	Strong transcription	Fetal Intestine Small	intestine
23	chr20:1420200-1430600	Strong transcription	Pancreas	Pancrea
24	chr20:1420200-1430600	Strong transcription	Right Ventricle	heart
25	chr20:1420200-1431200	Strong transcription	Primary B cells from cord blood	blood
26	chr20:1420200-1431400	Strong transcription	Left Ventricle	heart
27	chr20:1420200-1431600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr20:1420200-1431800	Strong transcription	Adipose Nuclei	Adipose
29	chr20:1420200-1431800	Strong transcription	Ovary	ovary
30	chr20:1420200-1437200	Strong transcription	Rectal Smooth Muscle	rectum
31	chr20:1420200-1444000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr20:1420200-1445600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr20:1420400-1430600	Strong transcription	Aorta	Aorta
34	chr20:1420400-1430600	Strong transcription	Spleen	Spleen
35	chr20:1420400-1430800	Strong transcription	Brain Angular Gyrus	brain
36	chr20:1420400-1430800	Strong transcription	Gastric	stomach
37	chr20:1420400-1431200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr20:1420400-1431800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr20:1420400-1431800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr20:1420400-1443600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr20:1420400-1444600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr20:1420400-1444800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr20:1420400-1445800	Strong transcription	A549	lung
44	chr20:1420600-1431400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr20:1420600-1431800	Strong transcription	Brain Substantia Nigra	brain
46	chr20:1420600-1431800	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr20:1420600-1444800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr20:1420800-1430600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr20:1421000-1430000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr20:1421000-1431000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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