Variant report

Variant	rs352166
Chromosome Location	chr3:52238677-52238678
allele	A/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	FOS	chr3:52238399-52239087	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr3:52238193-52239083	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr3:52238320-52239192	MCF10A-Er-Src	breast:	n/a	n/a
4	FOXA2	chr3:52238422-52238714	HepG2	liver:	n/a	n/a
5	JUND	chr3:52238494-52238722	HepG2	liver:	n/a	n/a
6	STAT3	chr3:52238258-52239115	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr3:52238317-52239151	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr3:52238332-52239066	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:52238560-52238694	GM12878	blood:	n/a	n/a
10	FOXA1	chr3:52238309-52238783	HepG2	liver:	n/a	chr3:52238565-52238580
11	FOXA1	chr3:52238407-52238787	HepG2	liver:	n/a	chr3:52238565-52238580
12	FOXA1	chr3:52238407-52238677	HepG2	liver:	n/a	chr3:52238565-52238580
13	STAT3	chr3:52238294-52239351	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr3:52238466-52239252	MCF10A-Er-Src	breast:	n/a	n/a
15	FOXA1	chr3:52238425-52238723	T-47D	breast:	n/a	chr3:52238565-52238580
16	CEBPB	chr3:52238490-52238819	HepG2	liver:	n/a	chr3:52238663-52238674
17	CEBPB	chr3:52238438-52238817	MCF-7	breast:	n/a	chr3:52238663-52238674
18	MYC	chr3:52238318-52239157	MCF10A-Er-Src	breast:	n/a	n/a
19	FOS	chr3:52238318-52239157	MCF10A-Er-Src	breast:	n/a	n/a
20	FOXA1	chr3:52238325-52238819	HepG2	liver:	n/a	chr3:52238565-52238580

No.	Distal block	Cell Line	Cell type
1	chr3:52230732..52234949-chr3:52236127..52239754,6	K562	blood:
2	chr3:52230039..52234196-chr3:52236127..52242387,6	K562	blood:
3	chr3:52237538..52239205-chr3:52267167..52269344,2	K562	blood:
4	chr3:52237147..52240103-chr3:52242583..52244871,3	MCF-7	breast:
5	chr3:52230948..52234705-chr3:52236612..52240056,5	MCF-7	breast:
6	chr3:52231540..52234351-chr3:52235459..52240031,5	MCF-7	breast:

Variant related genes	Relation type
ALAS1	TF binding region
ENSG00000023330	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs104903	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1060330	0.81[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap]
rs11712164	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs11717383	0.81[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap]
rs164640	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs181274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs187084	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs352139	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs352140	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs352158	0.96[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs352161	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs352162	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs352163	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352165	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs352167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352168	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs352169	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352170	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352171	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353547	0.81[CHB][hapmap]
rs353551	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs411457	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs524986	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs610060	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs614288	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6445358	0.81[CHB][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap]
rs6802320	0.88[ASN][1000 genomes]
rs730050	0.82[JPT][hapmap]
rs7614727	0.81[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap]
rs7622851	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs352166	GLT8D1	trans	brain	seeQTL
rs352166	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs352166	NEK4	cis	cerebellum	SCAN
rs352166	NEK4	cis	parietal	SCAN
rs352166	ITIH4	cis	parietal	SCAN
rs352166	NT5DC2	cis	lymphoblastoid	seeQTL
rs352166	GNL3	cis	cerebellum	SCAN
rs352166	SEMA3G	cis	parietal	SCAN
rs352166	DNAH1	cis	cerebellum	SCAN
rs352166	GLT8D1	cis	lymphoblastoid	seeQTL
rs352166	SPCS1	cis	parietal	SCAN
rs352166	FLJ12442	cis	multi-tissue	Pritchard
rs352166	GNL3	cis	parietal	SCAN
rs352166	GLYCTK	cis	multi-tissue	Pritchard
rs352166	GLT8D1	cis	brain	seeQTL
rs352166	RBM6	cis	cerebellum	SCAN
rs352166	SEMA3G	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52233000-52241600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:52233000-52245200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:52233400-52249600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:52233400-52249800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52233400-52250000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:52233400-52250000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:52233600-52238800	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:52233600-52239400	Strong transcription	Osteobl	bone
9	chr3:52233600-52249000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:52233600-52249200	Strong transcription	Fetal Muscle Leg	muscle
11	chr3:52233600-52249600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:52233600-52250000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:52233600-52250000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:52233600-52250000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:52233600-52250200	Strong transcription	Fetal Stomach	stomach
16	chr3:52233800-52249600	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:52233800-52250000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr3:52233800-52250400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:52234200-52239600	Strong transcription	NH-A	brain
20	chr3:52234400-52249800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr3:52234600-52239800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr3:52234600-52243200	Strong transcription	A549	lung
23	chr3:52234600-52249800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr3:52234600-52249800	Strong transcription	HSMM	muscle
25	chr3:52234600-52249800	Strong transcription	HUVEC	blood vessel
26	chr3:52234600-52250000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr3:52234800-52251000	Strong transcription	Fetal Brain Female	brain
28	chr3:52235000-52239000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:52235000-52250200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:52235200-52240600	Transcr. at gene 5' and 3'	Liver	Liver
31	chr3:52235200-52242800	Strong transcription	K562	blood
32	chr3:52235200-52246400	Strong transcription	NHDF-Ad	bronchial
33	chr3:52235200-52249200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:52235200-52249200	Strong transcription	Fetal Kidney	kidney
35	chr3:52235200-52249600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr3:52235200-52249800	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:52235400-52243200	Strong transcription	Hela-S3	cervix
38	chr3:52235400-52244200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:52235400-52249800	Strong transcription	Brain Cingulate Gyrus	brain
40	chr3:52235400-52250000	Strong transcription	Brain Germinal Matrix	brain
41	chr3:52235400-52250400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:52235600-52244200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:52235600-52248600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr3:52235600-52250000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:52235800-52240400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:52235800-52241000	Strong transcription	NHLF	lung
47	chr3:52235800-52244200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:52235800-52244200	Strong transcription	Fetal Lung	lung
49	chr3:52235800-52249400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:52235800-52249600	Strong transcription	Brain Anterior Caudate	brain

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