Variant report

Variant	rs1884389
Chromosome Location	chr20:1410582-1410583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1409886..1412172-chr20:1413671..1415589,2	K562	blood:
2	chr20:1408022..1413976-chr20:1445856..1450713,7	K562	blood:
3	chr20:1408581..1410916-chr20:1448637..1451105,2	K562	blood:
4	chr20:1408801..1411564-chr20:1423013..1426503,3	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1028508	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11087052	0.81[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11699735	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13063	0.90[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1884388	0.96[ASN][1000 genomes]
rs1884391	0.86[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2144542	0.90[ASN][1000 genomes]
rs2144543	0.90[ASN][1000 genomes]
rs2144544	0.83[ASN][1000 genomes]
rs2144545	0.92[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2144546	0.81[ASN][1000 genomes]
rs2207830	0.87[ASN][1000 genomes]
rs2317513	0.80[ASN][1000 genomes]
rs2317651	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2317652	0.91[CEU][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3088080	0.93[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3171292	0.90[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs3210915	0.90[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs36018423	0.90[ASN][1000 genomes]
rs3829698	0.82[CHD][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap]
rs4352285	0.93[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4546067	0.86[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4813133	0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4814229	0.82[ASN][1000 genomes]
rs4814237	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4814240	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4814243	0.82[CHD][hapmap]
rs4814244	0.93[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs5019244	0.90[ASN][1000 genomes]
rs6033697	0.82[ASN][1000 genomes]
rs6033698	0.82[ASN][1000 genomes]
rs6033709	0.82[ASN][1000 genomes]
rs6033710	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6033715	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6033726	0.90[ASN][1000 genomes]
rs6033728	0.90[ASN][1000 genomes]
rs6033729	0.90[ASN][1000 genomes]
rs6033732	0.90[ASN][1000 genomes]
rs6033744	0.90[ASN][1000 genomes]
rs6033807	0.93[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6042066	0.82[ASN][1000 genomes]
rs6042071	0.82[ASN][1000 genomes]
rs6042088	0.82[ASN][1000 genomes]
rs6042117	0.81[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6042118	0.81[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6042131	0.90[ASN][1000 genomes]
rs6042160	0.90[ASN][1000 genomes]
rs6042170	0.90[ASN][1000 genomes]
rs6042172	0.90[ASN][1000 genomes]
rs6042175	0.90[ASN][1000 genomes]
rs6042207	0.90[ASN][1000 genomes]
rs6042208	0.90[ASN][1000 genomes]
rs6042238	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6042244	0.90[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs6042268	0.83[ASN][1000 genomes]
rs6042270	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6042283	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6042292	0.90[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs6042354	0.90[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs6074623	0.83[ASN][1000 genomes]
rs6079133	0.88[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6079138	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6079139	0.83[ASN][1000 genomes]
rs6105102	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6105110	0.85[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs6105165	0.89[JPT][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6109893	0.90[ASN][1000 genomes]
rs6109894	0.90[ASN][1000 genomes]
rs6109912	0.90[ASN][1000 genomes]
rs6131468	0.82[ASN][1000 genomes]
rs6131506	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6131519	0.92[MEX][hapmap]
rs6134916	0.80[YRI][hapmap];0.90[ASN][1000 genomes]
rs6891	0.93[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs750424	0.90[ASN][1000 genomes]
rs8124053	0.81[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs910619	0.93[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs910620	0.93[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs932524	0.93[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9575	0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[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	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
rs1884389	NSFL1C	cis	Cerebellum	GTEx
rs1884389	NSFL1C	cis	cerebellum	SCAN
rs1884389	NSFL1C	Cis_1M	lymphoblastoid	RTeQTL
rs1884389	DEFB125	cis	cerebellum	SCAN
rs1884389	NSFL1C	cis	Frontal Cortex	GTEx
rs1884389	NSFL1C	cis	multi-tissue	Pritchard
rs1884389	NSFL1C	cis	Temporal Cortex	GTEx
rs1884389	NSFL1C	cis	lymphoblastoid	seeQTL
rs1884389	NSFL1C	cis	Brain Pons	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr20:1400000-1410600	Weak transcription	Osteobl	bone
3	chr20:1404600-1415600	Weak transcription	Brain Germinal Matrix	brain
4	chr20:1404800-1415200	Weak transcription	Brain Substantia Nigra	brain
5	chr20:1405000-1414600	Weak transcription	Thymus	Thymus
6	chr20:1405000-1420000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr20:1405400-1420000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
10	chr20:1407800-1410800	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
12	chr20:1408400-1411000	Enhancers	K562	blood
13	chr20:1408600-1414400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
15	chr20:1408800-1410600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr20:1408800-1410600	Weak transcription	Adipose Nuclei	Adipose
17	chr20:1408800-1410600	Weak transcription	NHDF-Ad	bronchial
18	chr20:1408800-1410800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr20:1408800-1414200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr20:1408800-1414400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr20:1408800-1415000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr20:1408800-1415800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr20:1408800-1417200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr20:1408800-1419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr20:1409000-1410600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr20:1409000-1410800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr20:1409000-1410800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr20:1409000-1410800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr20:1409000-1410800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr20:1409000-1411200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr20:1409000-1411200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr20:1409000-1411400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr20:1409000-1420200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr20:1409000-1420200	Weak transcription	Fetal Intestine Small	intestine
38	chr20:1409600-1410800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr20:1409600-1413400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr20:1409800-1411000	Enhancers	NHEK	skin
41	chr20:1409800-1411200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr20:1410000-1411000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr20:1410000-1411000	Enhancers	Fetal Intestine Large	intestine
44	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
45	chr20:1410200-1415000	Weak transcription	HMEC	breast
46	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
47	chr20:1410400-1411400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr20:1410400-1412000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr20:1410400-1412000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr20:1410400-1420400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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