Variant report

Variant	rs4621031
Chromosome Location	chr17:19550270-19550271
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	SP1	chr17:19549905-19551192	HCT-116	colon:	n/a	n/a
2	SP1	chr17:19550182-19552628	A549	lung:	n/a	chr17:19551974-19551986 chr17:19551975-19551984 chr17:19551971-19551985 chr17:19552030-19552051 chr17:19551974-19551986
3	MAX	chr17:19550054-19552808	A549	lung:	n/a	chr17:19551975-19551985 chr17:19552017-19552026 chr17:19551987-19551996 chr17:19552014-19552025 chr17:19552015-19552024
4	SMC3	chr17:19550185-19552968	Hela-S3	cervix:	n/a	chr17:19551892-19551902
5	NR2F2	chr17:19550234-19551126	MCF-7	breast:	n/a	n/a
6	SMARCC1	chr17:19550155-19552584	Hela-S3	cervix:	n/a	n/a
7	MYBL2	chr17:19550208-19550939	HepG2	liver:	n/a	n/a
8	SP1	chr17:19550108-19551088	HCT-116	colon:	n/a	n/a
9	FOSL1	chr17:19550110-19550896	HCT-116	colon:	n/a	n/a
10	EP300	chr17:19550063-19552788	ECC-1	luminal epithelium:	n/a	chr17:19551910-19551926 chr17:19551890-19551899 chr17:19551833-19551849 chr17:19551979-19551988
11	TCF7L2	chr17:19550228-19551017	HCT-116	colon:	n/a	n/a
12	TCF12	chr17:19550199-19550909	ECC-1	luminal epithelium:	n/a	n/a
13	TCF12	chr17:19550128-19552863	A549	lung:	n/a	n/a
14	GATA3	chr17:19550255-19551129	MCF-7	breast:	n/a	chr17:19550860-19550868
15	GATA3	chr17:19550138-19552752	A549	lung:	n/a	chr17:19550860-19550868
16	NR2F2	chr17:19550266-19550905	HepG2	liver:	n/a	n/a
17	FOXA1	chr17:19550235-19551186	HepG2	liver:	n/a	n/a
18	FOXA1	chr17:19550266-19551031	HepG2	liver:	n/a	n/a
19	MBD4	chr17:19550264-19550953	HepG2	liver:	n/a	n/a
20	FOXA1	chr17:19550194-19551106	HepG2	liver:	n/a	n/a
21	ZNF263	chr17:19550146-19552732	HEK293-T-REx	kidney:	n/a	n/a
22	FOSL2	chr17:19549752-19552795	A549	lung:	n/a	chr17:19550530-19550541
23	TEAD4	chr17:19550238-19551303	HepG2	liver:	n/a	n/a
24	MAX	chr17:19549955-19552795	HCT-116	colon:	n/a	chr17:19551975-19551985 chr17:19552017-19552026 chr17:19551987-19551996 chr17:19552014-19552025 chr17:19552015-19552024
25	SP1	chr17:19550219-19552660	A549	lung:	n/a	chr17:19551974-19551986 chr17:19551975-19551984 chr17:19551971-19551985 chr17:19552030-19552051 chr17:19551974-19551986
26	RCOR1	chr17:19550259-19552721	Hela-S3	cervix:	n/a	n/a
27	BCL3	chr17:19550085-19552757	A549	lung:	n/a	chr17:19551756-19551765 chr17:19551950-19551963 chr17:19551890-19551903 chr17:19551889-19551898 chr17:19552473-19552482
28	GABPA	chr17:19550180-19550779	A549	lung:	n/a	n/a
29	JUND	chr17:19550212-19550749	A549	lung:	n/a	chr17:19550529-19550540
30	NFIC	chr17:19550253-19550883	ECC-1	luminal epithelium:	n/a	n/a
31	FOSL1	chr17:19550046-19551198	HCT-116	colon:	n/a	n/a
32	MAX	chr17:19550252-19552780	A549	lung:	n/a	chr17:19551975-19551985 chr17:19552017-19552026 chr17:19551987-19551996 chr17:19552014-19552025 chr17:19552015-19552024
33	HDAC2	chr17:19550189-19551312	HepG2	liver:	n/a	chr17:19551021-19551035
34	EP300	chr17:19550196-19551463	HepG2	liver:	n/a	n/a
35	GTF2F1	chr17:19550079-19550947	Hela-S3	cervix:	n/a	n/a
36	EP300	chr17:19550200-19551040	Hela-S3	cervix:	n/a	n/a
37	NFIC	chr17:19550011-19550931	ECC-1	luminal epithelium:	n/a	n/a
38	JUND	chr17:19549951-19551073	HCT-116	colon:	n/a	chr17:19550529-19550540
39	EP300	chr17:19550185-19552788	A549	lung:	n/a	chr17:19551910-19551926 chr17:19551890-19551899 chr17:19551833-19551849 chr17:19551979-19551988
40	SIX5	chr17:19550094-19552259	A549	lung:	n/a	n/a
41	POLR2A	chr17:19550257-19550995	HCT-116	colon:	n/a	n/a
42	JUND	chr17:19550124-19551151	HCT-116	colon:	n/a	chr17:19550529-19550540
43	NFIC	chr17:19550259-19550826	HepG2	liver:	n/a	n/a
44	EP300	chr17:19550108-19551025	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19549675..19554690-chr17:19558689..19564889,9	MCF-7	breast:
2	chr17:19265973..19268468-chr17:19549750..19551918,2	MCF-7	breast:
3	chr17:19550266..19552397-chr17:19557719..19560014,2	MCF-7	breast:
4	chr17:19549032..19550747-chr17:19657076..19658934,2	MCF-7	breast:

Variant related genes	Relation type
ALDH3A2	TF binding region
ENSG00000230607	Chromatin interaction
ENSG00000072210	Chromatin interaction
ENSG00000108641	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1004490	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1004491	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1034897	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11204407	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11650399	0.86[CHD][hapmap]
rs12601634	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12604069	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12940877	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12945345	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16960251	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2120271	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28672254	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2891951	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35364675	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3752046	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3786038	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4244600	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4646793	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4646800	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4924788	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924791	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4925001	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4925002	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925026	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925037	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4925038	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4925040	0.84[AMR][1000 genomes]
rs4925041	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56262978	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58835440	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58970893	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61631401	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67870359	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68066777	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7216938	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73981559	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7502080	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs758427	0.81[GIH][hapmap]
rs962801	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs968012	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9902636	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9909886	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9914765	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][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	esv2757654	chr17:19485735-19563766	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv2758679	chr17:19485735-19563766	Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4621031	ALDH3A2	cis	parietal	SCAN
rs4621031	FLJ10847	cis	multi-tissue	Pritchard
rs4621031	ALDH3A2	cis	cerebellum	SCAN
rs4621031	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs4621031	ALDH3A2	cis	multi-tissue	Pritchard
rs4621031	ALDH3A2	cis	lymphoblastoid	seeQTL
rs4621031	MFAP4	cis	parietal	SCAN
rs4621031	TOM1L2	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19545600-19550400	Enhancers	HepG2	liver
2	chr17:19546200-19550400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr17:19547400-19551800	Flanking Active TSS	Liver	Liver
4	chr17:19548000-19551000	Enhancers	Stomach Mucosa	stomach
5	chr17:19548200-19550400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
6	chr17:19548200-19550800	Enhancers	Adipose Nuclei	Adipose
7	chr17:19548200-19550800	Enhancers	Osteobl	bone
8	chr17:19548200-19551000	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr17:19548400-19550400	Weak transcription	Placenta	Placenta
10	chr17:19548400-19550800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr17:19548400-19550800	Enhancers	Stomach Smooth Muscle	stomach
12	chr17:19548600-19550400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr17:19548800-19551000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr17:19548800-19551200	Enhancers	Fetal Heart	heart
15	chr17:19548800-19551600	Flanking Active TSS	Hela-S3	cervix
16	chr17:19549000-19550800	Enhancers	Duodenum Mucosa	Duodenum
17	chr17:19549400-19550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:19549400-19550400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr17:19549400-19550400	Weak transcription	Brain Substantia Nigra	brain
20	chr17:19549400-19550600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
21	chr17:19549400-19550600	Enhancers	Left Ventricle	heart
22	chr17:19549400-19551200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:19549400-19551200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr17:19549400-19551200	Enhancers	Pancreas	Pancrea
25	chr17:19549400-19551400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:19549600-19550400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr17:19549600-19550400	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr17:19549600-19550400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr17:19549600-19550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr17:19549600-19551000	Enhancers	H9 Cell Line	embryonic stem cell
31	chr17:19549600-19551000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr17:19549600-19551000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr17:19549600-19551200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:19549800-19550400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr17:19549800-19551000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:19549800-19551000	Enhancers	HMEC	breast
37	chr17:19549800-19551200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
38	chr17:19549800-19551200	Enhancers	Fetal Intestine Large	intestine
39	chr17:19549800-19551600	Flanking Active TSS	A549	lung
40	chr17:19550000-19550400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr17:19550000-19550600	Enhancers	HUVEC	blood vessel
42	chr17:19550000-19550600	Enhancers	NHDF-Ad	bronchial
43	chr17:19550000-19550800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr17:19550000-19550800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr17:19550000-19550800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:19550000-19550800	Enhancers	Brain Anterior Caudate	brain
47	chr17:19550000-19550800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr17:19550000-19550800	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr17:19550000-19550800	Enhancers	NHEK	skin
50	chr17:19550000-19550800	Enhancers	NHLF	lung

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