Variant report

Variant	rs4646798
Chromosome Location	chr17:19560656-19560657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr17:19560597-19560945	HepG2	liver:	n/a	n/a
2	FOXA1	chr17:19560579-19561038	HepG2	liver:	n/a	n/a
3	FOXA1	chr17:19560633-19560921	T-47D	breast:	n/a	n/a
4	ARID3A	chr17:19560630-19561122	HepG2	liver:	n/a	n/a
5	FOXA1	chr17:19560531-19560937	HepG2	liver:	n/a	n/a
6	FOXA2	chr17:19560625-19560921	HepG2	liver:	n/a	n/a
7	TEAD4	chr17:19560347-19561105	HepG2	liver:	n/a	n/a
8	HNF4A	chr17:19560627-19560876	HepG2	liver:	n/a	n/a
9	FOXA1	chr17:19560536-19561026	HepG2	liver:	n/a	n/a
10	ESR1	chr17:19560056-19560669	ECC-1	luminal epithelium:	n/a	n/a
11	EP300	chr17:19559974-19560717	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19549675..19554690-chr17:19558689..19564889,9	MCF-7	breast:
2	chr17:19558329..19562006-chr17:19563141..19565959,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252349	TF binding region
ALDH3A2	TF binding region
ENSG00000072210	Chromatin interaction
ENSG00000264932	Chromatin interaction
ENSG00000252349	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1004491	0.86[CHD][hapmap]
rs1025904	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1034896	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204407	0.86[CHD][hapmap]
rs11650399	0.94[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11653348	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12453452	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12453474	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12602112	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12603959	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12937179	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938816	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12949521	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1800869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1806922	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2072331	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072332	0.86[CHD][hapmap]
rs2072333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245724	0.81[EUR][1000 genomes]
rs2386144	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2891952	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34943952	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35797108	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35852749	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3786038	0.84[CHD][hapmap]
rs4598966	0.82[EUR][1000 genomes]
rs4646793	0.86[CHD][hapmap]
rs4646797	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925041	0.84[CHD][hapmap]
rs66462929	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71369434	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223468	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7503517	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8064748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8068713	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8073053	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8080672	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs962801	0.86[CHD][hapmap]
rs9797254	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9909440	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
8	nsv934250	chr17:19551657-19561421	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv933216	chr17:19555486-19561421	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	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
11	nsv907865	chr17:19558722-19575721	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4646798	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs4646798	MED9	cis	parietal	SCAN
rs4646798	ALDH3A2	cis	lymphoblastoid	seeQTL
rs4646798	FLJ10847	cis	multi-tissue	Pritchard
rs4646798	ALDH3A2	cis	multi-tissue	Pritchard
rs4646798	SMCR7	cis	cerebellum	SCAN
rs4646798	TOM1L2	cis	parietal	SCAN
rs4646798	ALDH3A2	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19553200-19566800	Weak transcription	Primary B cells from cord blood	blood
2	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:19553400-19566400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:19554800-19574400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr17:19555000-19561400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr17:19555000-19561400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:19555000-19563400	Strong transcription	Fetal Stomach	stomach
9	chr17:19555000-19568800	Weak transcription	NH-A	brain
10	chr17:19555000-19581800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr17:19555000-19582800	Weak transcription	HUVEC	blood vessel
12	chr17:19555200-19566400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr17:19555200-19566600	Weak transcription	NHDF-Ad	bronchial
14	chr17:19555200-19569800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr17:19555200-19576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr17:19555400-19570000	Strong transcription	Fetal Muscle Leg	muscle
17	chr17:19555600-19562200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:19555600-19567200	Weak transcription	Right Atrium	heart
19	chr17:19555600-19569800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:19555600-19578600	Weak transcription	Small Intestine	intestine
21	chr17:19555800-19560800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:19555800-19560800	Strong transcription	Left Ventricle	heart
23	chr17:19555800-19561000	Strong transcription	Fetal Brain Female	brain
24	chr17:19555800-19561600	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr17:19555800-19562400	Strong transcription	Brain Hippocampus Middle	brain
26	chr17:19556000-19561400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr17:19556200-19560800	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr17:19556200-19561200	Strong transcription	Colonic Mucosa	Colon
29	chr17:19556200-19569800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr17:19556400-19561200	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr17:19556400-19563600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr17:19556600-19562200	Strong transcription	Adipose Nuclei	Adipose
33	chr17:19556600-19569800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr17:19556800-19560800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr17:19556800-19560800	Strong transcription	Spleen	Spleen
36	chr17:19557200-19569800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr17:19557600-19561200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr17:19557800-19561000	Genic enhancers	Liver	Liver
39	chr17:19558000-19560800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr17:19558000-19560800	Strong transcription	Rectal Smooth Muscle	rectum
41	chr17:19558000-19561200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr17:19558000-19561400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr17:19558000-19562200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr17:19558000-19563600	Strong transcription	HMEC	breast
45	chr17:19558200-19560800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr17:19558200-19560800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:19558200-19560800	Strong transcription	Brain Substantia Nigra	brain
48	chr17:19558200-19562400	Genic enhancers	HepG2	liver
49	chr17:19558200-19568200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr17:19558200-19569400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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