Variant report

Variant	rs3795135
Chromosome Location	chr20:1441841-1441842
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:1441725-1442089	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:1429669..1432038-chr20:1440054..1444992,4	K562	blood:
2	chr20:1432252..1433910-chr20:1441547..1444195,2	K562	blood:
3	chr20:1440240..1443130-chr20:1446363..1447888,2	MCF-7	breast:

Variant related genes	Relation type
NSFL1C	TF binding region
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1028508	0.84[ASN][1000 genomes]
rs11699735	0.84[ASN][1000 genomes]
rs13063	0.81[ASN][1000 genomes]
rs1543423	0.85[JPT][hapmap]
rs1884391	0.80[ASN][1000 genomes]
rs2144544	0.80[ASN][1000 genomes]
rs2144545	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2317652	0.84[ASN][1000 genomes]
rs2317653	0.81[AMR][1000 genomes]
rs3088080	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3171292	0.81[ASN][1000 genomes]
rs3210915	0.81[ASN][1000 genomes]
rs3795134	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3829698	0.86[CHB][hapmap]
rs4352285	0.81[ASN][1000 genomes]
rs4546067	0.81[ASN][1000 genomes]
rs6033807	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs6033858	0.87[ASN][1000 genomes]
rs6033860	0.80[JPT][hapmap]
rs6033867	0.85[JPT][hapmap]
rs6042238	0.84[ASN][1000 genomes]
rs6042244	0.80[ASN][1000 genomes]
rs6042268	0.80[ASN][1000 genomes]
rs6042270	0.80[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs6042283	0.84[ASN][1000 genomes]
rs6042292	0.81[ASN][1000 genomes]
rs6042354	0.80[ASN][1000 genomes]
rs6074626	0.82[AMR][1000 genomes]
rs6074631	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6079133	0.93[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs6079138	0.84[ASN][1000 genomes]
rs6079139	0.81[ASN][1000 genomes]
rs6079294	0.85[JPT][hapmap]
rs6105165	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6131506	0.84[ASN][1000 genomes]
rs6135033	0.95[JPT][hapmap]
rs6135060	0.85[JPT][hapmap]
rs6135061	0.80[JPT][hapmap]
rs6891	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs910619	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs910620	0.81[ASN][1000 genomes]
rs932524	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs9575	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs963867	0.85[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3795135	NSFL1C	cis	Temporal Cortex	GTEx
rs3795135	SIRPB2	cis	lung	GTEx
rs3795135	NSFL1C	cis	Cerebellum	GTEx
rs3795135	NSFL1C	cis	Brain Pons	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1419200-1443400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr20:1419600-1442000	Strong transcription	Skeletal Muscle Male	skeletal muscle
3	chr20:1419800-1443600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr20:1420200-1444000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr20:1420200-1445600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr20:1420400-1443600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr20:1420400-1444600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr20:1420400-1444800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:1420400-1445800	Strong transcription	A549	lung
10	chr20:1420600-1444800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr20:1421200-1444400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr20:1421400-1445200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr20:1421400-1446000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:1421600-1444200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr20:1421600-1445800	Strong transcription	Placenta	Placenta
16	chr20:1421800-1442600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr20:1421800-1445800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr20:1422000-1444800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr20:1422400-1442400	Strong transcription	Colonic Mucosa	Colon
20	chr20:1422400-1442600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr20:1422400-1444800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr20:1422600-1442000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr20:1422600-1444200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr20:1422800-1442800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr20:1422800-1444800	Strong transcription	HUVEC	blood vessel
26	chr20:1423000-1443800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr20:1423200-1444600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr20:1429200-1442000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr20:1431600-1446400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr20:1432400-1444000	Strong transcription	Left Ventricle	heart
31	chr20:1432400-1444400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr20:1432600-1442200	Strong transcription	HepG2	liver
33	chr20:1432600-1443000	Strong transcription	Fetal Thymus	thymus
34	chr20:1432600-1443400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr20:1432600-1443800	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr20:1432600-1444400	Strong transcription	Lung	lung
37	chr20:1432600-1445000	Strong transcription	Liver	Liver
38	chr20:1432800-1442400	Strong transcription	Adipose Nuclei	Adipose
39	chr20:1432800-1444000	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr20:1432800-1444600	Strong transcription	Primary T cells from cord blood	blood
41	chr20:1432800-1445800	Strong transcription	Fetal Intestine Large	intestine
42	chr20:1433000-1443000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr20:1433000-1444200	Strong transcription	Brain Hippocampus Middle	brain
44	chr20:1433000-1444800	Strong transcription	NHEK	skin
45	chr20:1433200-1445400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr20:1433200-1445800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr20:1433400-1445200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr20:1433400-1445600	Strong transcription	Brain Germinal Matrix	brain
49	chr20:1433400-1445800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr20:1433600-1446600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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