Variant report

Variant	rs3802762
Chromosome Location	chr11:45672261-45672262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:45672248-45672298	HL-60	blood:	n/a
2	chr11:45672248-45672298	HUVEC	blood vessel:	n/a
3	chr11:45672248-45672298	HNPCEpiC	eye:	n/a
4	chr11:45672248-45672298	Hepatocyte	liver:	n/a
5	chr11:45672248-45672298	ProgFib	skin:	n/a
6	chr11:45672248-45672298	RPTEC	kidney:	n/a
7	chr11:45672248-45672298	AG04450	lung:	fetal
8	chr11:45672248-45672298	GM12891	blood:	n/a
9	chr11:45672248-45672298	NHBE	bronchial:	n/a
10	chr11:45672248-45672298	CMK	blood:	n/a
11	chr11:45672248-45672298	NHDF-neo	bronchial:	n/a
12	chr11:45672248-45672298	SK-N-SH	brain:	n/a
13	chr11:45672248-45672298	ECC-1	luminal epithelium:	n/a
14	chr11:45672248-45672298	A549	lung:	n/a
15	chr11:45672248-45672298	GM19239	blood:	n/a
16	chr11:45672248-45672298	AG09319	gingival:	n/a
17	chr11:45672248-45672298	AG09309	skin:	n/a
18	chr11:45672248-45672298	GM12892	blood:	n/a
19	chr11:45672248-45672298	HepG2	liver:	n/a
20	chr11:45672248-45672298	HEK293	kidney:	embryo
21	chr11:45672248-45672298	SK-N-MC	brain:	n/a
22	chr11:45672248-45672298	HAEpiC	amniotic membrane:	n/a
23	chr11:45672248-45672298	GM06990	blood:	n/a
24	chr11:45672248-45672298	SKMC	muscle:	n/a
25	chr11:45672248-45672298	AoSMC	blood vessel:	n/a
26	chr11:45672248-45672298	MCF10A-Er-Src	breast:	n/a
27	chr11:45672248-45672298	HPAEpiC	pulmonary alveolar:	n/a
28	chr11:45672248-45672298	SAEC	small airway:	n/a
29	chr11:45672248-45672298	Caco-2	colon:	n/a
30	chr11:45672248-45672298	NB4	blood:	n/a
31	chr11:45672248-45672298	PFSK-1	brain:	n/a
32	chr11:45672248-45672298	Jurkat	blood:	n/a
33	chr11:45672248-45672298	Hela-S3	cervix:	n/a
34	chr11:45672248-45672298	PrEC	prostate:	n/a
35	chr11:45672248-45672298	SK-N-SH_RA	brain:	n/a
36	chr11:45672248-45672298	IMR90	lung:	fetal
37	chr11:45672248-45672298	HIPEpiC	eye:	n/a
38	chr11:45672248-45672298	GM12878	blood:	n/a
39	chr11:45672248-45672298	HCM	heart:	n/a
40	chr11:45672248-45672298	U87	brain:	n/a
41	chr11:45672248-45672298	HEEpiC	esophagus:	n/a
42	chr11:45672248-45672298	AG10803	skin:	n/a
43	chr11:45672248-45672298	AG04449	skin:	fetal
44	chr11:45672248-45672298	BJ	skin:	n/a
45	chr11:45672248-45672298	HCF	heart:	n/a
46	chr11:45672248-45672298	K562	blood:	n/a
47	chr11:45672248-45672298	HCPEpiC	choroid plexus:	n/a
48	chr11:45672248-45672298	ovcar-3	ovarian:	n/a
49	chr11:45672248-45672298	PANC-1	pancreas:	n/a
50	chr11:45672248-45672298	HRPEpiC	eye:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45671225..45673031-chr11:45675062..45677985,2	K562	blood:

No data

Variant related genes	Relation type
CHST1	CpG island
ENSG00000255091	CpG island

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10838503	0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs11038595	0.90[ASN][1000 genomes]
rs11038602	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11038604	0.97[ASN][1000 genomes]
rs11038605	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1992849	0.93[ASN][1000 genomes]
rs2277272	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3740702	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4148898	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148902	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4540819	0.90[ASN][1000 genomes]
rs4755331	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66798082	0.80[ASN][1000 genomes]
rs72896778	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897311	chr11:45663568-45691118	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv897312	chr11:45663568-45699134	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv897313	chr11:45670395-45699134	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3802762	CHST1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45665600-45674400	Weak transcription	HMEC	breast
2	chr11:45665600-45680000	Weak transcription	Gastric	stomach
3	chr11:45669200-45674000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:45669800-45673200	Weak transcription	Brain Angular Gyrus	brain
5	chr11:45669800-45676400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:45669800-45676400	Weak transcription	HUVEC	blood vessel
7	chr11:45669800-45676600	Weak transcription	Left Ventricle	heart
8	chr11:45670000-45672800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:45670000-45680200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:45670200-45673800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:45670600-45672600	Strong transcription	Aorta	Aorta
12	chr11:45670600-45673200	Strong transcription	Ovary	ovary
13	chr11:45670600-45673800	Strong transcription	Fetal Brain Female	brain
14	chr11:45670600-45675400	Strong transcription	Dnd41	blood
15	chr11:45670600-45676600	Weak transcription	Brain Hippocampus Middle	brain
16	chr11:45671000-45673000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:45671200-45672600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:45671200-45672800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:45671200-45673000	ZNF genes & repeats	Spleen	Spleen
20	chr11:45671200-45673200	Strong transcription	Brain Cingulate Gyrus	brain
21	chr11:45671200-45673400	Strong transcription	Brain Anterior Caudate	brain
22	chr11:45671200-45673400	Strong transcription	Lung	lung
23	chr11:45671200-45676200	Weak transcription	Fetal Brain Male	brain
24	chr11:45671400-45672400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:45671400-45672400	Strong transcription	Right Ventricle	heart
26	chr11:45671800-45673600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:45671800-45674200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:45672000-45673600	Strong transcription	Brain Germinal Matrix	brain
29	chr11:45672000-45673800	Weak transcription	Fetal Muscle Leg	muscle
30	chr11:45672200-45672400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:45672200-45673400	Strong transcription	Brain Inferior Temporal Lobe	brain

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