Variant report

Variant	rs3744489
Chromosome Location	chr17:67138138-67138139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:67137535-67138914	MCF10A-Er-Src	breast:	n/a	n/a
2	NFYB	chr17:67137905-67138348	Hela-S3	cervix:	n/a	chr17:67138295-67138308
3	STAT3	chr17:67137909-67138146	MCF10A-Er-Src	breast:	n/a	n/a
4	YY1	chr17:67137932-67138140	K562	blood:	n/a	n/a
5	IRF1	chr17:67137877-67138293	K562	blood:	n/a	chr17:67138222-67138239
6	POLR2A	chr17:67137906-67138246	HUVEC	blood vessel:	n/a	n/a
7	E2F4	chr17:67137951-67138235	MCF10A-Er-Src	breast:	n/a	chr17:67138200-67138214
8	YY1	chr17:67137882-67138429	SK-N-SH	brain:	n/a	chr17:67138246-67138268 chr17:67138258-67138268
9	FOXA1	chr17:67137999-67138412	HepG2	liver:	n/a	n/a
10	MYC	chr17:67137969-67138231	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr17:67137623-67138921	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr17:67137691-67138959	HUVEC	blood vessel:	n/a	n/a
13	STAT3	chr17:67137801-67138896	MCF10A-Er-Src	breast:	n/a	chr17:67138265-67138273
14	FOS	chr17:67137928-67138220	MCF10A-Er-Src	breast:	n/a	chr17:67138122-67138131
15	STAT3	chr17:67137909-67138196	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:67138138-67138188	Hela-S3	cervix:	n/a
2	chr17:67138138-67138188	SK-N-SH	brain:	n/a
3	chr17:67138138-67138188	HPAEpiC	pulmonary alveolar:	n/a
4	chr17:67138138-67138188	Caco-2	colon:	n/a
5	chr17:67138138-67138188	CMK	blood:	n/a
6	chr17:67138138-67138188	HRE	kidney:	n/a
7	chr17:67138138-67138188	GM19239	blood:	n/a
8	chr17:67138138-67138188	HEK293	kidney:	embryo
9	chr17:67138138-67138188	RPTEC	kidney:	n/a
10	chr17:67138138-67138188	SAEC	small airway:	n/a
11	chr17:67138138-67138188	A549	lung:	n/a
12	chr17:67138138-67138188	HMEC	breast:	n/a
13	chr17:67138138-67138188	ovcar-3	ovarian:	n/a
14	chr17:67138138-67138188	IMR90	lung:	fetal
15	chr17:67138138-67138188	SK-N-MC	brain:	n/a
16	chr17:67138138-67138188	SK-N-SH_RA	brain:	n/a
17	chr17:67138138-67138188	K562	blood:	n/a
18	chr17:67138138-67138188	GM12878	blood:	n/a
19	chr17:67138138-67138188	AG09309	skin:	n/a
20	chr17:67138138-67138188	NB4	blood:	n/a
21	chr17:67138138-67138188	HCT-116	colon:	n/a
22	chr17:67138138-67138188	ProgFib	skin:	n/a
23	chr17:67138138-67138188	HL-60	blood:	n/a
24	chr17:67138138-67138188	Jurkat	blood:	n/a
25	chr17:67138138-67138188	HIPEpiC	eye:	n/a
26	chr17:67138138-67138188	HRCEpiC	kidney:	n/a
27	chr17:67138138-67138188	LNCaP	prostate:	n/a
28	chr17:67138138-67138188	NHDF-neo	bronchial:	n/a
29	chr17:67138138-67138188	HCM	heart:	n/a
30	chr17:67138138-67138188	H1-hESC	embryonic stem cell:	embryo
31	chr17:67138138-67138188	SKMC	muscle:	n/a
32	chr17:67138138-67138188	HepG2	liver:	n/a
33	chr17:67138138-67138188	AG04449	skin:	fetal
34	chr17:67138138-67138188	PFSK-1	brain:	n/a
35	chr17:67138138-67138188	PANC-1	pancreas:	n/a
36	chr17:67138138-67138188	AG09319	gingival:	n/a
37	chr17:67138138-67138188	MCF-7	breast:	n/a
38	chr17:67138138-67138188	BJ	skin:	n/a
39	chr17:67138138-67138188	HCPEpiC	choroid plexus:	n/a
40	chr17:67138138-67138188	AG04450	lung:	fetal
41	chr17:67138138-67138188	AoSMC	blood vessel:	n/a
42	chr17:67138138-67138188	HNPCEpiC	eye:	n/a
43	chr17:67138138-67138188	HEEpiC	esophagus:	n/a
44	chr17:67138138-67138188	GM06990	blood:	n/a
45	chr17:67138138-67138188	HRPEpiC	eye:	n/a
46	chr17:67138138-67138188	PrEC	prostate:	n/a
47	chr17:67138138-67138188	ECC-1	luminal epithelium:	n/a
48	chr17:67138138-67138188	T-47D	breast:	n/a
49	chr17:67138138-67138188	HCF	heart:	n/a
50	chr17:67138138-67138188	Hepatocyte	liver:	n/a

No data

Variant related genes	Relation type
ABCA6	TF binding region
ABCA6	CpG island

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10775358	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10775359	0.81[ASN][1000 genomes]
rs1158495	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11652530	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11656539	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11659091	0.81[TSI][hapmap]
rs12162136	0.84[EUR][1000 genomes]
rs12453914	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12601388	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12939282	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12940298	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12952117	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12953127	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1558166	0.84[ASN][1000 genomes]
rs16973567	0.86[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1968100	0.83[ASN][1000 genomes]
rs1974575	0.84[YRI][hapmap]
rs1974576	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1974577	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1990335	0.84[EUR][1000 genomes]
rs2041170	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2041171	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108738	0.81[ASN][1000 genomes]
rs2190900	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2215148	0.84[ASN][1000 genomes]
rs2364986	0.84[ASN][1000 genomes]
rs2364993	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4141177	0.84[CEU][hapmap];0.86[CHB][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4334355	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4577157	0.82[ASN][1000 genomes]
rs4603621	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968785	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4968838	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968839	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968843	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4968849	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs4968851	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs5025273	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs6501183	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207609	0.84[EUR][1000 genomes]
rs7208586	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7210259	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7213831	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7214079	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7216899	0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7217887	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs740518	0.84[ASN][1000 genomes]
rs740520	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7503217	0.84[EUR][1000 genomes]
rs763920	0.83[TSI][hapmap]
rs8064595	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8066449	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs8074654	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs8077252	0.86[CHB][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs8077551	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs8078314	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8079981	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8080863	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9303012	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs976698	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs981452	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9892172	0.83[ASN][1000 genomes]
rs9898868	0.83[ASN][1000 genomes]
rs9899837	0.83[ASN][1000 genomes]
rs9902643	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9904672	0.83[ASN][1000 genomes]
rs9911770	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9912127	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs9916084	0.81[ASN][1000 genomes]
rs9916693	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs997781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv470598	chr17:67081830-67212595	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv575930	chr17:67120025-67212031	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3744489	MRC2	cis	parietal	SCAN
rs3744489	ABCA9	cis	parietal	SCAN
rs3744489	ABCA6	cis	parietal	SCAN
rs3744489	CACNG5	cis	cerebellum	SCAN
rs3744489	ABCA6	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67096200-67143400	Weak transcription	Psoas Muscle	Psoas
2	chr17:67101200-67143400	Weak transcription	Pancreas	Pancrea
3	chr17:67114600-67162800	Weak transcription	Brain Angular Gyrus	brain
4	chr17:67124800-67150000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:67127000-67143400	Weak transcription	Fetal Intestine Large	intestine
6	chr17:67127000-67150600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:67130600-67146200	Weak transcription	Lung	lung
8	chr17:67132000-67151600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr17:67133800-67145600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr17:67134400-67143400	Weak transcription	Left Ventricle	heart
11	chr17:67134600-67145000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr17:67136200-67138800	Active TSS	Ovary	ovary
13	chr17:67136200-67138800	Active TSS	Right Atrium	heart
14	chr17:67136200-67139000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:67136400-67138800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:67136600-67138200	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr17:67136600-67138600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr17:67136600-67138800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr17:67136600-67138800	Active TSS	Fetal Lung	lung
20	chr17:67136800-67138800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr17:67136800-67138800	Active TSS	Stomach Smooth Muscle	stomach
22	chr17:67137000-67138200	Active TSS	Fetal Muscle Leg	muscle
23	chr17:67137200-67138400	Active TSS	Colon Smooth Muscle	Colon
24	chr17:67137200-67138600	Active TSS	Brain Substantia Nigra	brain
25	chr17:67137400-67138600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr17:67137400-67138600	Flanking Active TSS	Osteobl	bone
27	chr17:67137600-67138400	Flanking Active TSS	NHLF	lung
28	chr17:67137600-67138600	Active TSS	Brain Anterior Caudate	brain
29	chr17:67137600-67138600	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr17:67137600-67138600	Flanking Active TSS	HUVEC	blood vessel
31	chr17:67137600-67139000	Enhancers	HepG2	liver
32	chr17:67137600-67139200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr17:67137800-67138200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr17:67137800-67138200	Active TSS	Brain Cingulate Gyrus	brain
35	chr17:67137800-67138200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr17:67137800-67138200	Active TSS	Duodenum Mucosa	Duodenum
37	chr17:67137800-67138200	ZNF genes & repeats	Fetal Brain Male	brain
38	chr17:67137800-67138200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr17:67137800-67138200	Enhancers	K562	blood
40	chr17:67137800-67138400	Enhancers	Fetal Kidney	kidney
41	chr17:67137800-67138800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:67137800-67138800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr17:67137800-67138800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr17:67137800-67138800	Enhancers	HMEC	breast
45	chr17:67137800-67141200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr17:67137800-67141400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr17:67138000-67138200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr17:67138000-67138200	Flanking Active TSS	Fetal Stomach	stomach
49	chr17:67138000-67138200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr17:67138000-67138600	Enhancers	Stomach Mucosa	stomach

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