Variant report

Variant	rs3761896
Chromosome Location	chr20:12989901-12989902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:102)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:102 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:12989880-12990030	AoAF	blood vessel:	n/a	n/a
2	CTCF	chr20:12989856-12990015	MCF-7	breast:	n/a	n/a
3	MYBL2	chr20:12989295-12991152	HepG2	liver:	n/a	n/a
4	FOS	chr20:12989580-12990657	MCF10A-Er-Src	breast:	n/a	chr20:12990571-12990580
5	CTCF	chr20:12989860-12990010	HCPEpiC	choroid plexus:	n/a	n/a
6	CTCF	chr20:12989863-12990021	NHEK	skin:	n/a	n/a
7	RAD21	chr20:12989716-12990166	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr20:12989860-12990010	HPAF	blood vessel:	n/a	n/a
9	CTCF	chr20:12989900-12990050	HPF	lung:	n/a	n/a
10	CTCF	chr20:12989866-12989999	Pancreas_OC	pancreas:	n/a	n/a
11	CTCF	chr20:12989840-12989990	RPTEC	kidney:	n/a	n/a
12	CTCF	chr20:12989860-12990010	HCFaa	heart:	n/a	n/a
13	GATA3	chr20:12989489-12989981	T-47D	breast:	n/a	n/a
14	FOXA1	chr20:12989463-12990070	T-47D	breast:	n/a	n/a
15	CTCF	chr20:12989800-12989950	HRPEpiC	eye:	n/a	n/a
16	CTCF	chr20:12989856-12989999	LNCaP	prostate:	n/a	n/a
17	CTCF	chr20:12989820-12989970	HRPEpiC	eye:	n/a	n/a
18	RAD21	chr20:12989706-12990192	MCF-7	breast:	n/a	n/a
19	RAD21	chr20:12989543-12990157	HepG2	liver:	n/a	n/a
20	CTCF	chr20:12989860-12990010	Caco-2	colon:	n/a	n/a
21	CTCF	chr20:12989726-12990071	T-47D	breast:	n/a	n/a
22	CTCF	chr20:12989827-12990051	MCF-7	breast:	n/a	n/a
23	CTCF	chr20:12989840-12989990	HAc	cerebellar:	n/a	n/a
24	STAT3	chr20:12989801-12989997	MCF10A-Er-Src	breast:	n/a	n/a
25	RAD21	chr20:12989421-12990233	HepG2	liver:	n/a	n/a
26	CTCF	chr20:12989900-12990050	MCF-7	breast:	n/a	n/a
27	CTCF	chr20:12989853-12989997	MCF-7	breast:	n/a	n/a
28	CTCF	chr20:12989840-12989990	AG04449	skin:	n/a	n/a
29	CTCF	chr20:12989880-12990030	GM12873	blood:	n/a	n/a
30	CTCF	chr20:12989854-12989988	MCF-7	breast:	n/a	n/a
31	POLR2A	chr20:12989435-12990964	MCF10A-Er-Src	breast:	n/a	n/a
32	SMC3	chr20:12989542-12990312	HepG2	liver:	n/a	n/a
33	RAD21	chr20:12989695-12990123	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr20:12989814-12990109	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr20:12989800-12989950	AG09319	gingival:	n/a	n/a
36	CTCF	chr20:12989840-12989990	HepG2	liver:	n/a	n/a
37	CTCF	chr20:12989840-12989990	HA-sp	spinal cord:	n/a	n/a
38	POLR2A	chr20:12989605-12990006	MCF-7	breast:	n/a	n/a
39	CTCF	chr20:12989840-12989990	Caco-2	colon:	n/a	n/a
40	CTCF	chr20:12989740-12990030	HVMF	connective:	n/a	n/a
41	CTCF	chr20:12989840-12989990	AG10803	skin:	n/a	n/a
42	CTCF	chr20:12989898-12989971	Hela-S3	cervix:	n/a	n/a
43	EP300	chr20:12989524-12990006	T-47D	breast:	n/a	n/a
44	MAFK	chr20:12989752-12989961	HepG2	liver:	n/a	n/a
45	CTCF	chr20:12989743-12990029	H1-hESC	embryonic stem cell:	n/a	n/a
46	RAD21	chr20:12989663-12990102	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr20:12989782-12990026	GM12878	blood:	n/a	n/a
48	CTCF	chr20:12989820-12989970	HEEpiC	esophagus:	n/a	n/a
49	SMC3	chr20:12989837-12989924	GM12878	blood:	n/a	n/a
50	CTCF	chr20:12989820-12989970	HFF-Myc	foreskin:	n/a	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPTLC3-3	chr20:12989627-12990032	NONHSAT078677

No data

Variant related genes	Relation type
SPTLC3	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11698429	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs12479968	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12481402	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1367743	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs17190775	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17190782	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17190927	1.00[ASW][hapmap]
rs2236124	1.00[ASW][hapmap]
rs2327446	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3761894	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843767	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3859619	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4813104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55646676	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58975911	0.84[ASN][1000 genomes]
rs6033574	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs6041799	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs6074543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6074544	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6074545	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6074564	1.00[ASW][hapmap]
rs6078872	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6078875	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6078877	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6078880	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs6078886	0.82[ASN][1000 genomes]
rs6078887	0.83[ASN][1000 genomes]
rs6078889	0.84[ASN][1000 genomes]
rs6078890	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6078891	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6078895	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6078899	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv833923	chr20:12904689-13064426	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3761896	SEL1L2	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12988000-12997600	Weak transcription	Hela-S3	cervix
2	chr20:12989200-12990000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr20:12989200-12990000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr20:12989200-12990200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr20:12989200-12990800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:12989200-12990800	Active TSS	Fetal Kidney	kidney
7	chr20:12989200-12991200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr20:12989200-12991400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr20:12989400-12990000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr20:12989400-12990000	Active TSS	Adipose Nuclei	Adipose
11	chr20:12989400-12990000	Enhancers	GM12878-XiMat	blood
12	chr20:12989400-12990000	Active TSS	HSMMtube	muscle
13	chr20:12989400-12990000	Active TSS	Osteobl	bone
14	chr20:12989400-12990200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr20:12989400-12990200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:12989400-12990200	Active TSS	NH-A	brain
17	chr20:12989400-12990400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr20:12989400-12990400	Active TSS	Primary T cells from cord blood	blood
19	chr20:12989400-12990400	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr20:12989400-12990400	Active TSS	A549	lung
21	chr20:12989400-12990400	Active TSS	HMEC	breast
22	chr20:12989400-12990600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr20:12989400-12990600	Active TSS	Duodenum Mucosa	Duodenum
24	chr20:12989400-12990600	Active TSS	Stomach Smooth Muscle	stomach
25	chr20:12989400-12990600	Active TSS	HSMM	muscle
26	chr20:12989400-12990800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr20:12989400-12990800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr20:12989400-12990800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr20:12989400-12990800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr20:12989400-12990800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr20:12989400-12990800	Active TSS	Aorta	Aorta
32	chr20:12989400-12990800	Active TSS	Brain Angular Gyrus	brain
33	chr20:12989400-12990800	Active TSS	Brain Anterior Caudate	brain
34	chr20:12989400-12990800	Active TSS	Fetal Muscle Trunk	muscle
35	chr20:12989400-12990800	Active TSS	Placenta	Placenta
36	chr20:12989400-12990800	Active TSS	Pancreas	Pancrea
37	chr20:12989400-12990800	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr20:12989400-12990800	Active TSS	Rectal Smooth Muscle	rectum
39	chr20:12989400-12990800	Active TSS	Right Atrium	heart
40	chr20:12989400-12990800	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr20:12989400-12990800	Active TSS	NHDF-Ad	bronchial
42	chr20:12989400-12990800	Active TSS	NHLF	lung
43	chr20:12989400-12991000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr20:12989400-12992000	Active TSS	Fetal Intestine Small	intestine
45	chr20:12989400-12992600	Active TSS	Fetal Intestine Large	intestine
46	chr20:12989600-12990000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr20:12989600-12990000	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr20:12989600-12990000	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr20:12989600-12990000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr20:12989600-12990000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

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