Variant report

Variant	rs932524
Chromosome Location	chr20:1420336-1420337
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:1413774..1421620-chr20:1445657..1450800,12	K562	blood:
2	chr20:1418150..1421031-chr20:1445969..1448576,3	MCF-7	breast:
3	chr20:1413566..1416812-chr20:1419779..1424298,4	K562	blood:
4	chr20:1419982..1421924-chr20:1432480..1435232,2	K562	blood:
5	chr20:1418037..1419774-chr20:1420141..1424100,3	MCF-7	breast:
6	chr20:1418229..1420990-chr20:1423275..1425647,2	MCF-7	breast:
7	chr20:1417607..1420469-chr20:1423578..1425297,2	K562	blood:
8	chr20:1419111..1421909-chr20:1426787..1429297,2	MCF-7	breast:
9	chr20:1370272..1370827-chr20:1420141..1420942,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1028508	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11087052	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs11699735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs1884388	0.83[ASN][1000 genomes]
rs1884389	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]
rs1884391	0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2144544	0.95[ASN][1000 genomes]
rs2144545	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2144546	0.84[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs2317513	0.93[ASN][1000 genomes]
rs2317651	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2317652	0.91[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3088080	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3171292	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3210915	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3795135	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3829698	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap];0.93[ASN][1000 genomes]
rs4352285	0.92[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4546067	0.92[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4813133	0.84[JPT][hapmap]
rs4814237	0.89[JPT][hapmap]
rs4814240	0.89[JPT][hapmap]
rs4814244	0.87[CHD][hapmap];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[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042117	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs6042118	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs6042238	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042244	0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6042268	0.95[ASN][1000 genomes]
rs6042270	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042283	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6042292	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6042354	0.92[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6074631	0.83[ASN][1000 genomes]
rs6079133	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]
rs6079138	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079139	0.96[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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6131506	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6131519	0.92[CEU][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6134916	0.80[YRI][hapmap]
rs6891	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124053	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs910619	0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs910620	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9575	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:5 , 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
5	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs932524	NSFL1C	cis	Temporal Cortex	GTEx
rs932524	NSFL1C	cis	brain	seeQTL
rs932524	NSFL1C	cis	Frontal Cortex	GTEx
rs932524	NSFL1C	cis	Liver	GTEx
rs932524	NSFL1C	cis	Cerebellum	GTEx
rs932524	NSFL1C	cis	multi-tissue	Pritchard
rs932524	NSFL1C	cis	parietal	SCAN
rs932524	NSFL1C	cis	lymphoblastoid	seeQTL
rs932524	NSFL1C	cis	Brain Pons	GTEx
rs932524	NSFL1C	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr20:1405400-1420400	Weak transcription	Brain Angular Gyrus	brain
3	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
4	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
5	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
9	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
10	chr20:1410400-1420400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr20:1411000-1422400	Weak transcription	Psoas Muscle	Psoas
12	chr20:1411200-1420600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr20:1411200-1421200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr20:1411800-1420400	Weak transcription	Aorta	Aorta
15	chr20:1413200-1422600	Weak transcription	Fetal Kidney	kidney
16	chr20:1413800-1420400	Weak transcription	Gastric	stomach
17	chr20:1413800-1424200	Weak transcription	Colon Smooth Muscle	Colon
18	chr20:1415200-1422800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr20:1415400-1420400	Weak transcription	Fetal Lung	lung
20	chr20:1415400-1421800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr20:1415400-1422400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr20:1415400-1422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr20:1415600-1420400	Weak transcription	A549	lung
24	chr20:1415600-1422600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr20:1415600-1423200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr20:1415800-1420600	Weak transcription	Brain Substantia Nigra	brain
27	chr20:1415800-1422000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr20:1416000-1420400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr20:1416000-1420600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr20:1416000-1421000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr20:1416000-1421000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr20:1416000-1421600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr20:1416000-1422000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr20:1416000-1422000	Weak transcription	HSMM	muscle
35	chr20:1416000-1422000	Weak transcription	NH-A	brain
36	chr20:1416000-1422200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr20:1416000-1422400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr20:1416000-1422400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr20:1416000-1422400	Weak transcription	Small Intestine	intestine
40	chr20:1416200-1420400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr20:1416200-1420600	Weak transcription	NHLF	lung
42	chr20:1416200-1420800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr20:1416200-1421600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr20:1416200-1421800	Weak transcription	HMEC	breast
45	chr20:1416200-1422200	Weak transcription	HSMMtube	muscle
46	chr20:1416200-1422600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr20:1416200-1422600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr20:1416200-1422600	Weak transcription	NHEK	skin
49	chr20:1416200-1423200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr20:1416400-1420400	Weak transcription	Primary monocytes fromperipheralblood	blood

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