Variant report

Variant	rs516803
Chromosome Location	chr11:58695112-58695113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr11:58694784-58695492	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:58694591-58696288	H1-hESC	embryonic stem cell:	n/a	n/a
3	FOXA1	chr11:58694663-58695208	T-47D	breast:	n/a	n/a
4	TAF1	chr11:58694671-58695628	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP1	chr11:58694797-58695399	H1-hESC	embryonic stem cell:	n/a	chr11:58695087-58695098 chr11:58695027-58695039 chr11:58695027-58695039 chr11:58695028-58695037 chr11:58695029-58695038
6	POLR2A	chr11:58694755-58695580	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:58694813-58696075	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr11:58694894-58696015	H1-hESC	embryonic stem cell:	n/a	n/a
9	ATF2	chr11:58694851-58695251	H1-hESC	embryonic stem cell:	n/a	n/a
10	GTF2F1	chr11:58694881-58695308	H1-hESC	embryonic stem cell:	n/a	n/a
11	CHD2	chr11:58694884-58695809	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr11:58694817-58695325	H1-hESC	embryonic stem cell:	n/a	n/a
13	YY1	chr11:58694811-58695289	H1-hESC	embryonic stem cell:	n/a	chr11:58695078-58695097
14	YY1	chr11:58694771-58695196	H1-hESC	embryonic stem cell:	n/a	chr11:58695078-58695097
15	TAF1	chr11:58694762-58695225	H1-hESC	embryonic stem cell:	n/a	n/a
16	KAP1	chr11:58694887-58695668	U2OS	brain:	n/a	n/a
17	FOXA1	chr11:58694741-58695236	T-47D	breast:	n/a	n/a
18	TBP	chr11:58694805-58695978	H1-hESC	embryonic stem cell:	n/a	n/a
19	SIN3A	chr11:58694814-58695936	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAFK	chr11:58694852-58695650	H1-hESC	embryonic stem cell:	n/a	n/a
21	SP1	chr11:58694715-58695473	H1-hESC	embryonic stem cell:	n/a	chr11:58695087-58695098 chr11:58695027-58695039 chr11:58695027-58695039 chr11:58695028-58695037 chr11:58695029-58695038
22	MAX	chr11:58694773-58695259	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:58695093-58695143	HUVEC	blood vessel:	n/a
2	chr11:58695093-58695143	HPAEpiC	pulmonary alveolar:	n/a
3	chr11:58695093-58695143	HEK293	kidney:	embryo
4	chr11:58695093-58695143	NHBE	bronchial:	n/a
5	chr11:58695093-58695143	NH-A	brain:	n/a
6	chr11:58695093-58695143	BE2_C	brain:	n/a
7	chr11:58695093-58695143	HRE	kidney:	n/a
8	chr11:58695093-58695143	ovcar-3	ovarian:	n/a
9	chr11:58695093-58695143	Jurkat	blood:	n/a
10	chr11:58695093-58695143	AG09319	gingival:	n/a
11	chr11:58695093-58695143	SK-N-MC	brain:	n/a
12	chr11:58695093-58695143	HL-60	blood:	n/a
13	chr11:58695093-58695143	HMEC	breast:	n/a
14	chr11:58695093-58695143	AG10803	skin:	n/a
15	chr11:58695093-58695143	Hela-S3	cervix:	n/a
16	chr11:58695093-58695143	HCT-116	colon:	n/a
17	chr11:58695093-58695143	HNPCEpiC	eye:	n/a
18	chr11:58695093-58695143	CMK	blood:	n/a
19	chr11:58695093-58695143	NB4	blood:	n/a
20	chr11:58695093-58695143	AG09309	skin:	n/a
21	chr11:58695093-58695143	MCF-7	breast:	n/a
22	chr11:58695093-58695143	GM12892	blood:	n/a
23	chr11:58695093-58695143	T-47D	breast:	n/a
24	chr11:58695093-58695143	LNCaP	prostate:	n/a
25	chr11:58695093-58695143	PANC-1	pancreas:	n/a
26	chr11:58695093-58695143	H1-hESC	embryonic stem cell:	embryo
27	chr11:58695093-58695143	SAEC	small airway:	n/a
28	chr11:58695093-58695143	HRPEpiC	eye:	n/a
29	chr11:58695093-58695143	AG04449	skin:	fetal
30	chr11:58695093-58695143	HepG2	liver:	n/a
31	chr11:58695093-58695143	GM19239	blood:	n/a
32	chr11:58695093-58695143	SK-N-SH	brain:	n/a
33	chr11:58695093-58695143	PrEC	prostate:	n/a
34	chr11:58695093-58695143	AoSMC	blood vessel:	n/a
35	chr11:58695093-58695143	HCM	heart:	n/a
36	chr11:58695093-58695143	U87	brain:	n/a
37	chr11:58695093-58695143	HAEpiC	amniotic membrane:	n/a
38	chr11:58695093-58695143	SKMC	muscle:	n/a
39	chr11:58695093-58695143	BJ	skin:	n/a
40	chr11:58695093-58695143	IMR90	lung:	fetal
41	chr11:58695093-58695143	PFSK-1	brain:	n/a
42	chr11:58695093-58695143	A549	lung:	n/a
43	chr11:58695093-58695143	MCF10A-Er-Src	breast:	n/a
44	chr11:58695093-58695143	HCF	heart:	n/a
45	chr11:58695093-58695143	GM06990	blood:	n/a
46	chr11:58695093-58695143	SK-N-SH_RA	brain:	n/a
47	chr11:58695093-58695143	ProgFib	skin:	n/a
48	chr11:58695093-58695143	HRCEpiC	kidney:	n/a
49	chr11:58695093-58695143	AG04450	lung:	fetal
50	chr11:58695093-58695143	NT2-D1	testis:	n/a

No data

Variant related genes	Relation type
GLYATL1	TF binding region
GLYATL1	CpG island

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11229690	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11229707	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11603726	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1788552	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1892866	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1938785	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1938787	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1938788	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2005121	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2105736	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2156322	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs474121	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs478587	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs478705	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs480196	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs482219	0.80[CHD][hapmap]
rs482751	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs483991	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs486507	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs488446	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs489782	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs489846	0.94[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];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs501703	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs510360	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs513677	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs530481	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs532318	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs533087	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs535218	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs538472	0.92[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs544687	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs546051	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs550864	0.88[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs563370	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs564335	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs573271	0.81[JPT][hapmap]
rs574058	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs576790	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7120597	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv3444895	chr11:58614102-58779384	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv3445007	chr11:58638330-58709867	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3502182	chr11:58668199-58731237	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3502181	chr11:58668236-58731215	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3478019	chr11:58668282-58731214	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3478030	chr11:58668282-58731214	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3502183	chr11:58668353-58731177	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3393019	chr11:58679419-58880845	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs516803	FADS3	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58691000-58695200	Weak transcription	Stomach Mucosa	stomach
2	chr11:58691200-58695200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr11:58691200-58695200	Weak transcription	Colonic Mucosa	Colon
4	chr11:58691200-58695200	Weak transcription	Fetal Lung	lung
5	chr11:58691600-58695800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:58692200-58695200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:58692400-58695200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:58693400-58695800	Enhancers	NH-A	brain
9	chr11:58693600-58695800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:58693800-58695800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr11:58694000-58695200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:58694000-58695800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:58694000-58696000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:58694400-58695400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:58694400-58696200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:58694600-58695200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr11:58694600-58695400	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr11:58694600-58695600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr11:58694600-58696000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr11:58694600-58696000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:58694800-58695200	Active TSS	Primary T cells from cord blood	blood
22	chr11:58694800-58695200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:58694800-58695200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr11:58694800-58695200	Flanking Active TSS	Pancreas	Pancrea
25	chr11:58694800-58695200	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr11:58694800-58695200	Active TSS	Thymus	Thymus
27	chr11:58694800-58695400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:58694800-58695400	Active TSS	Fetal Brain Male	brain
29	chr11:58694800-58695400	Active TSS	Psoas Muscle	Psoas
30	chr11:58694800-58695400	Bivalent Enhancer	HepG2	liver
31	chr11:58694800-58695600	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr11:58694800-58695600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr11:58694800-58695600	Active TSS	Brain Germinal Matrix	brain
34	chr11:58694800-58695600	Flanking Active TSS	Fetal Brain Female	brain
35	chr11:58694800-58695800	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr11:58694800-58695800	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr11:58694800-58695800	Enhancers	HMEC	breast
38	chr11:58694800-58696000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:58694800-58696000	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr11:58694800-58696000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr11:58694800-58696000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:58694800-58696000	Enhancers	Esophagus	oesophagus
43	chr11:58694800-58696000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr11:58694800-58696000	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr11:58694800-58696000	Enhancers	NHEK	skin
46	chr11:58694800-58696200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:58694800-58696200	Enhancers	Primary B cells from peripheral blood	blood
48	chr11:58694800-58696200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:58694800-58696200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:58694800-58696200	Flanking Active TSS	Duodenum Mucosa	Duodenum

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