Variant report

Variant	rs4925038
Chromosome Location	chr17:19576078-19576079
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	RAD21	chr17:19575250-19576086	HepG2	liver:	n/a	chr17:19575953-19575966
2	RAD21	chr17:19575779-19576101	H1-hESC	embryonic stem cell:	n/a	chr17:19575953-19575966
3	CTCF	chr17:19575940-19576090	AG04450	lung:	n/a	n/a
4	RAD21	chr17:19575772-19576116	IMR90	lung:	n/a	chr17:19575953-19575966
5	RAD21	chr17:19575665-19576084	A549	lung:	n/a	chr17:19575953-19575966
6	RAD21	chr17:19575716-19576086	MCF-7	breast:	n/a	chr17:19575953-19575966
7	SMC3	chr17:19575348-19576088	HepG2	liver:	n/a	n/a
8	RAD21	chr17:19575722-19576098	ECC-1	luminal epithelium:	n/a	chr17:19575953-19575966
9	SMC3	chr17:19575786-19576086	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr17:19575784-19576110	K562	blood:	n/a	n/a
11	CTCF	chr17:19575940-19576090	HCM	heart:	n/a	n/a
12	RAD21	chr17:19575800-19576110	Hela-S3	cervix:	n/a	chr17:19575953-19575966
13	RAD21	chr17:19575600-19576104	MCF-7	breast:	n/a	chr17:19575953-19575966
14	RAD21	chr17:19575645-19576184	SK-N-SH	brain:	n/a	chr17:19575953-19575966
15	CTCF	chr17:19575797-19576128	IMR90	lung:	n/a	n/a
16	RAD21	chr17:19575643-19576101	HCT-116	colon:	n/a	chr17:19575953-19575966
17	RAD21	chr17:19575244-19576125	HepG2	liver:	n/a	chr17:19575953-19575966
18	CTCF	chr17:19575704-19576160	HCT-116	colon:	n/a	n/a
19	RAD21	chr17:19575772-19576097	HepG2	liver:	n/a	chr17:19575953-19575966
20	CTCF	chr17:19575801-19576191	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19265895..19266829-chr17:19575547..19576368,3	MCF-7	breast:
2	chr17:19550468..19552548-chr17:19574981..19577039,2	MCF-7	breast:

Variant related genes	Relation type
ALDH3A2	TF binding region
ENSG00000108641	Chromatin interaction
ENSG00000072210	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1004490	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1004491	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034897	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204407	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12601634	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12604069	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12940877	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12945345	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16960251	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2072332	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2120271	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28672254	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2891951	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35364675	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786038	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4244600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4621031	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646793	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646800	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924788	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4924791	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4925002	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4925026	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4925037	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925040	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4925041	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56262978	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58970893	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61631401	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68066777	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73981559	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7502080	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs962801	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968012	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9902636	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9909886	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9914765	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv1062485	chr17:19558644-19608008	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4925038	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs4925038	ALDH3A2	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
5	chr17:19555200-19576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
7	chr17:19558400-19579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:19559600-19578600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:19559800-19577200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr17:19564000-19581000	Weak transcription	Thymus	Thymus
11	chr17:19567600-19578600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:19567600-19584800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:19567800-19578600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr17:19568400-19581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr17:19568600-19606800	Weak transcription	Psoas Muscle	Psoas
16	chr17:19569000-19582000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:19569400-19577000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:19569600-19578600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr17:19569600-19579000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:19569600-19584000	Weak transcription	Placenta	Placenta
21	chr17:19569800-19578600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:19569800-19578600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr17:19569800-19591000	Weak transcription	Fetal Brain Male	brain
24	chr17:19570000-19578800	Weak transcription	Colonic Mucosa	Colon
25	chr17:19570000-19579200	Weak transcription	Aorta	Aorta
26	chr17:19572400-19576600	Strong transcription	Brain Germinal Matrix	brain
27	chr17:19572600-19582800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr17:19572800-19576200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr17:19572800-19580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:19572800-19583000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr17:19574000-19576200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr17:19574200-19576200	Genic enhancers	Fetal Muscle Leg	muscle
33	chr17:19574200-19576400	Genic enhancers	Brain Cingulate Gyrus	brain
34	chr17:19574200-19576600	Strong transcription	Primary T cells from cord blood	blood
35	chr17:19574200-19577200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr17:19574200-19577800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr17:19574200-19579000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr17:19574200-19580600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:19574200-19582400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr17:19574400-19576200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr17:19574400-19576200	Enhancers	Right Atrium	heart
42	chr17:19574400-19577400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
43	chr17:19574400-19578600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr17:19574600-19576200	Genic enhancers	Rectal Mucosa Donor 31	rectum
45	chr17:19574600-19576800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr17:19574600-19576800	Enhancers	Fetal Intestine Large	intestine
47	chr17:19574600-19577600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr17:19574600-19579000	Weak transcription	Ovary	ovary
49	chr17:19574800-19576200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr17:19574800-19577600	Enhancers	Stomach Mucosa	stomach

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