Variant report

Variant	rs1810132
Chromosome Location	chr17:37866005-37866006
allele	C/T
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	chr17:37865902-37866091	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr17:37865495-37866201	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:37815487..37818092-chr17:37864402..37866827,2	MCF-7	breast:
2	chr17:37843168..37845541-chr17:37863729..37866216,2	MCF-7	breast:
3	chr17:37843552..37845628-chr17:37864708..37866273,2	K562	blood:
4	chr17:37864069..37866883-chr17:37884219..37886655,3	MCF-7	breast:

Variant related genes	Relation type
ERBB2	TF binding region
ENSG00000141736	Chromatin interaction
ENSG00000131748	Chromatin interaction
ENSG00000161395	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1058808	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11653998	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12150298	0.80[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.84[MEX][hapmap]
rs12150603	0.81[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap]
rs12940986	0.81[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.80[MEX][hapmap]
rs14050	0.90[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap]
rs1476278	0.81[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.80[MEX][hapmap]
rs1565922	0.87[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap]
rs1565923	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2088126	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247862	0.90[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap]
rs2313171	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs2517951	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2517954	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs2517955	0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs2517956	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2517957	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2517958	0.81[CEU][hapmap];0.82[CHB][hapmap];0.80[JPT][hapmap]
rs2643194	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2643195	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2904766	0.81[ASN][1000 genomes]
rs2934952	0.94[CEU][hapmap]
rs2934953	0.90[CEU][hapmap];0.83[CHB][hapmap]
rs2934967	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934971	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941503	0.95[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap]
rs2941504	0.90[CEU][hapmap];0.83[CHB][hapmap];0.96[MEX][hapmap]
rs2941505	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs2941506	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2941520	0.85[EUR][1000 genomes]
rs2952151	0.90[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap]
rs2952155	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2952156	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952157	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4252627	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4795393	0.82[ASN][1000 genomes]
rs8078228	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs903501	0.90[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs903502	0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.88[MEX][hapmap]
rs903506	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907087	0.90[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap]
rs907089	0.81[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.80[MEX][hapmap]
rs9303274	0.81[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.80[MEX][hapmap]
rs9675194	0.81[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.84[MEX][hapmap]
rs9972882	0.83[GIH][hapmap];0.81[TSI][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	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv528093	chr17:37814080-37866005	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS 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	nsv1056234	chr17:37862605-37909988	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv908216	chr17:37863015-37879588	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	nsv908217	chr17:37863708-37879588	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1810132	PGAP3	cis	Muscle Skeletal	GTEx
rs1810132	MED24	cis	parietal	SCAN
rs1810132	GSDMB	cis	cerebellum	SCAN
rs1810132	PGAP3	cis	Heart Left Ventricle	GTEx
rs1810132	PGAP3	cis	Stomach	GTEx
rs1810132	DHRS11	cis	cerebellum	SCAN
rs1810132	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs1810132	SLFN14	cis	parietal	SCAN
rs1810132	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs1810132	PGAP3	cis	cerebellum	SCAN
rs1810132	PNMT	cis	parietal	SCAN
rs1810132	SPACA3	cis	parietal	SCAN
rs1810132	PGAP3	cis	Thyroid	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37857000-37872000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr17:37858000-37885200	Weak transcription	Fetal Brain Male	brain
3	chr17:37858000-37885600	Weak transcription	Hela-S3	cervix
4	chr17:37858200-37882600	Weak transcription	NHDF-Ad	bronchial
5	chr17:37858400-37879600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:37859400-37881000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr17:37861400-37883600	Weak transcription	Brain Substantia Nigra	brain
8	chr17:37862200-37866600	Enhancers	Primary T cells fromperipheralblood	blood
9	chr17:37862200-37877000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr17:37862200-37885200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr17:37862400-37876800	Strong transcription	HepG2	liver
12	chr17:37862400-37877600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:37862400-37878800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr17:37862400-37885400	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr17:37862400-37885600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:37862400-37885600	Strong transcription	Fetal Stomach	stomach
17	chr17:37862400-37885800	Weak transcription	Right Atrium	heart
18	chr17:37862600-37866200	Genic enhancers	Placenta	Placenta
19	chr17:37862600-37866800	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr17:37862600-37871400	Weak transcription	HSMM	muscle
21	chr17:37862600-37871600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:37862600-37885600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr17:37862800-37866600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr17:37862800-37872000	Weak transcription	NH-A	brain
25	chr17:37862800-37878800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:37862800-37883200	Weak transcription	Small Intestine	intestine
27	chr17:37862800-37885600	Strong transcription	Fetal Intestine Large	intestine
28	chr17:37863000-37868800	Strong transcription	A549	lung
29	chr17:37863000-37869400	Strong transcription	Adipose Nuclei	Adipose
30	chr17:37863000-37870000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:37863000-37872400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr17:37863000-37873800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr17:37863000-37876600	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr17:37863000-37877000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:37863000-37878800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr17:37863000-37879000	Strong transcription	HSMMtube	muscle
37	chr17:37863000-37879600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr17:37863000-37885600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr17:37863200-37867000	Strong transcription	NHLF	lung
40	chr17:37863200-37868800	Strong transcription	Aorta	Aorta
41	chr17:37863200-37869200	Strong transcription	Ovary	ovary
42	chr17:37863200-37869400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr17:37863200-37876800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr17:37863200-37879400	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr17:37863200-37885600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr17:37863200-37885800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr17:37863400-37866400	Weak transcription	Brain Hippocampus Middle	brain
48	chr17:37863400-37867000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:37863400-37868800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr17:37863400-37869200	Strong transcription	Fetal Kidney	kidney

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