Variant report

Variant	rs737452
Chromosome Location	chr3:46027410-46027411
allele	A/G
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	FOXA2	chr3:46027403-46027796	A549	lung:	n/a	n/a
2	CTCF	chr3:46027280-46027430	HCPEpiC	choroid plexus:	n/a	n/a
3	MXI1	chr3:46027214-46028786	IMR90	lung:	n/a	n/a
4	CTCF	chr3:46027260-46027410	AG09309	skin:	n/a	n/a
5	FOXA2	chr3:46027406-46028408	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46008363..46011066-chr3:46026720..46029201,2	MCF-7	breast:
2	chr3:46026501..46029475-chr3:46032165..46035137,4	MCF-7	breast:

Variant related genes	Relation type
FYCO1	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1072755	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs11130080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12485978	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12495073	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12630101	0.96[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12635494	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12635657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639598	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13060901	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13066048	0.96[CEU][hapmap]
rs13073861	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1392290	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1392291	0.91[ASN][1000 genomes]
rs1491959	0.82[CHB][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap]
rs1500005	0.80[ASN][1000 genomes]
rs1546077	0.82[CHB][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap]
rs1546079	1.00[LWK][hapmap]
rs1552489	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs1552490	0.80[EUR][1000 genomes]
rs1601867	0.81[ASN][1000 genomes]
rs17078495	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994488	0.80[EUR][1000 genomes]
rs1994490	0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2054866	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2131091	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap]
rs2234358	0.81[ASN][1000 genomes]
rs2248228	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2373154	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs28808964	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34381514	0.80[ASN][1000 genomes]
rs35465473	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35537559	1.00[ASN][1000 genomes]
rs3733097	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733100	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3733103	0.88[CEU][hapmap]
rs3774634	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs3774635	0.80[EUR][1000 genomes]
rs3774639	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs3796375	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3796376	0.82[CHD][hapmap]
rs3821883	0.83[ASN][1000 genomes]
rs3821884	0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3851347	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4234452	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4333119	0.80[ASN][1000 genomes]
rs4535265	0.96[CEU][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs4682800	0.84[JPT][hapmap]
rs4682810	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4683148	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap]
rs4683156	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683157	0.96[CEU][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs59226168	1.00[ASN][1000 genomes]
rs60539039	0.89[ASN][1000 genomes]
rs62242796	1.00[ASN][1000 genomes]
rs67044455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764042	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6778896	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780163	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6781668	0.83[ASN][1000 genomes]
rs6795629	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6805094	0.83[ASN][1000 genomes]
rs6809381	0.85[CHB][hapmap]
rs7129	0.88[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap]
rs730983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751553	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7616464	0.80[ASN][1000 genomes]
rs7623460	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7643426	0.85[CHB][hapmap]
rs931704	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936938	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs9824253	0.80[EUR][1000 genomes]
rs9824886	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs9831315	0.92[CEU][hapmap]
rs9849015	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs737452	CXCR6	cis	parietal	SCAN
rs737452	UBA7	cis	parietal	SCAN
rs737452	CDC25A	cis	cerebellum	SCAN
rs737452	CCDC71	cis	cerebellum	SCAN
rs737452	CXCR6	cis	Muscle Skeletal	GTEx
rs737452	NCKIPSD	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46000000-46029600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:46009000-46027800	Weak transcription	Fetal Brain Male	brain
3	chr3:46010200-46029600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:46010200-46033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
6	chr3:46015800-46027600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:46016200-46027800	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr3:46019400-46030000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:46020000-46034200	Genic enhancers	Dnd41	blood
10	chr3:46021400-46028200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:46021400-46036200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:46021600-46034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:46022600-46027600	Strong transcription	GM12878-XiMat	blood
14	chr3:46022600-46028000	Strong transcription	Primary B cells from cord blood	blood
15	chr3:46023000-46029800	Strong transcription	Primary T cells from cord blood	blood
16	chr3:46023200-46027600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:46023200-46028200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:46025000-46029400	Genic enhancers	Fetal Intestine Small	intestine
19	chr3:46025000-46031600	Weak transcription	Fetal Kidney	kidney
20	chr3:46025200-46031800	Enhancers	Right Atrium	heart
21	chr3:46025400-46027600	Weak transcription	Small Intestine	intestine
22	chr3:46025400-46027800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:46025400-46028000	Strong transcription	Thymus	Thymus
24	chr3:46025600-46027600	Genic enhancers	Fetal Stomach	stomach
25	chr3:46025600-46028000	Weak transcription	NHEK	skin
26	chr3:46025600-46032400	Enhancers	Stomach Mucosa	stomach
27	chr3:46025600-46033000	Enhancers	Right Ventricle	heart
28	chr3:46025800-46028400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:46025800-46031200	Enhancers	HSMMtube	muscle
30	chr3:46026000-46028200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:46026000-46028800	Enhancers	Aorta	Aorta
32	chr3:46026000-46031800	Enhancers	NHDF-Ad	bronchial
33	chr3:46026200-46027800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:46026200-46027800	Weak transcription	Brain Angular Gyrus	brain
35	chr3:46026200-46028600	Enhancers	Brain Germinal Matrix	brain
36	chr3:46026200-46029800	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr3:46026200-46031800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr3:46026200-46032000	Enhancers	Ovary	ovary
39	chr3:46026200-46032000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr3:46026200-46032000	Enhancers	NHLF	lung
41	chr3:46026400-46027600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:46026400-46027600	Enhancers	HepG2	liver
43	chr3:46026400-46027800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:46026400-46028000	Weak transcription	Hela-S3	cervix
45	chr3:46026400-46028200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr3:46026400-46028400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:46026400-46029200	Enhancers	Adipose Nuclei	Adipose
48	chr3:46026400-46029400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:46026400-46029400	Enhancers	Fetal Lung	lung
50	chr3:46026400-46031400	Enhancers	HSMM	muscle

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