Variant report

Variant	rs11030404
Chromosome Location	chr11:3980638-3980639
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	EBF1	chr11:3980550-3981007	GM12878	blood:	n/a	chr11:3980746-3980757
2	FOSL2	chr11:3980249-3980997	A549	lung:	n/a	n/a
3	BCL11A	chr11:3980620-3980915	GM12878	blood:	n/a	n/a
4	RAD21	chr11:3980173-3980687	HCT-116	colon:	n/a	n/a
5	NR3C1	chr11:3980623-3981109	A549	lung:	n/a	chr11:3980928-3980942
6	SMC3	chr11:3980339-3980685	GM12878	blood:	n/a	chr11:3980468-3980476
7	BCL11A	chr11:3980575-3980988	GM12878	blood:	n/a	n/a
8	CTCF	chr11:3980282-3980645	K562	blood:	n/a	chr11:3980466-3980475 chr11:3980462-3980475
9	RFX5	chr11:3980453-3980891	HepG2	liver:	n/a	n/a
10	GATA3	chr11:3980456-3981659	A549	lung:	n/a	chr11:3980760-3980769
11	RAD21	chr11:3980243-3980699	A549	lung:	n/a	n/a
12	ARID3A	chr11:3980313-3981498	HepG2	liver:	n/a	n/a
13	FOS	chr11:3980581-3980958	MCF10A-Er-Src	breast:	n/a	n/a
14	TEAD4	chr11:3980614-3981689	HepG2	liver:	n/a	n/a
15	CTCF	chr11:3980308-3980647	GM12878	blood:	n/a	chr11:3980466-3980475 chr11:3980462-3980475
16	CTCF	chr11:3980379-3980643	IMR90	lung:	n/a	chr11:3980466-3980475 chr11:3980462-3980475
17	FOS	chr11:3980577-3980943	MCF10A-Er-Src	breast:	n/a	n/a
18	RAD21	chr11:3980293-3980638	GM12878	blood:	n/a	n/a
19	GATA3	chr11:3980396-3981001	SK-N-SH	brain:	n/a	chr11:3980760-3980769
20	CTCF	chr11:3980285-3980638	K562	blood:	n/a	chr11:3980466-3980475 chr11:3980462-3980475
21	FOSL2	chr11:3980504-3981015	SK-N-SH	brain:	n/a	n/a
22	RAD21	chr11:3980215-3980692	A549	lung:	n/a	n/a
23	CTCF	chr11:3980089-3981320	A549	lung:	n/a	chr11:3980466-3980475 chr11:3980462-3980475
24	CTCF	chr11:3980248-3980675	A549	lung:	n/a	chr11:3980466-3980475 chr11:3980462-3980475
25	ARID3A	chr11:3980359-3980683	K562	blood:	n/a	n/a
26	IRF4	chr11:3980527-3980932	GM12878	blood:	n/a	n/a
27	EBF1	chr11:3980531-3980975	GM12878	blood:	n/a	chr11:3980746-3980757
28	FOS	chr11:3980599-3981160	MCF10A-Er-Src	breast:	n/a	n/a
29	CTCF	chr11:3980500-3980650	GM12873	blood:	n/a	n/a
30	CTCF	chr11:3980317-3980660	MCF-7	breast:	n/a	chr11:3980466-3980475 chr11:3980462-3980475
31	EBF1	chr11:3980609-3980970	GM12878	blood:	n/a	chr11:3980746-3980757
32	RAD21	chr11:3980310-3980640	HepG2	liver:	n/a	n/a
33	CUX1	chr11:3980347-3980736	K562	blood:	n/a	n/a
34	RUNX3	chr11:3980491-3981040	GM12878	blood:	n/a	n/a
35	FOS	chr11:3980611-3980945	MCF10A-Er-Src	breast:	n/a	n/a
36	SMC3	chr11:3980304-3981095	HepG2	liver:	n/a	chr11:3980468-3980476
37	IRF1	chr11:3980355-3980705	K562	blood:	n/a	chr11:3980528-3980542 chr11:3980532-3980542 chr11:3980530-3980543 chr11:3980484-3980501 chr11:3980533-3980544
38	NFIC	chr11:3980502-3981060	GM12878	blood:	n/a	chr11:3980582-3980610
39	MAFK	chr11:3980512-3980719	K562	blood:	n/a	n/a
40	RAD21	chr11:3980308-3980666	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr11:3980247-3980661	HepG2	liver:	n/a	n/a
42	JUN	chr11:3980411-3980751	K562	blood:	n/a	n/a
43	RUNX3	chr11:3980531-3980993	GM12878	blood:	n/a	n/a
44	CTCF	chr11:3980268-3980647	K562	blood:	n/a	chr11:3980466-3980475 chr11:3980462-3980475
45	IRF1	chr11:3980353-3980677	K562	blood:	n/a	chr11:3980528-3980542 chr11:3980532-3980542 chr11:3980530-3980543 chr11:3980484-3980501 chr11:3980533-3980544
46	TBL1XR1	chr11:3980423-3980727	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:3979407..3982038-chr11:3982601..3985547,3	K562	blood:
2	chr11:3870179..3871112-chr11:3980205..3980923,2	K562	blood:
3	chr11:3875728..3877004-chr11:3979944..3980979,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255232	TF binding region
ENSG00000167323	Chromatin interaction
ENSG00000229368	Chromatin interaction
ENSG00000228661	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1013351	0.85[EUR][1000 genomes]
rs10500590	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs10742200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10767702	0.85[EUR][1000 genomes]
rs10767706	0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap]
rs10767713	0.86[EUR][1000 genomes]
rs10767715	0.87[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs10767720	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10767721	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767723	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767767	0.87[GIH][hapmap];0.87[TSI][hapmap]
rs10767811	0.83[GIH][hapmap];0.88[TSI][hapmap]
rs10835311	0.85[EUR][1000 genomes]
rs10835312	0.83[EUR][1000 genomes]
rs10835320	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835324	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835331	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10835333	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835337	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835340	0.87[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10835359	0.87[EUR][1000 genomes]
rs10835390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835399	0.87[EUR][1000 genomes]
rs10835402	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs10835403	0.87[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs10835406	0.87[EUR][1000 genomes]
rs10835407	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs10835508	0.84[YRI][hapmap]
rs10835596	0.83[GIH][hapmap];0.90[TSI][hapmap]
rs11030276	0.85[EUR][1000 genomes]
rs11030599	0.80[EUR][1000 genomes]
rs11030639	0.89[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs11030781	0.83[GIH][hapmap];0.90[TSI][hapmap]
rs11493482	0.81[EUR][1000 genomes]
rs1155146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11828337	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12223176	0.88[EUR][1000 genomes]
rs12270732	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12281293	0.87[EUR][1000 genomes]
rs12283447	0.87[EUR][1000 genomes]
rs12286710	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs12290747	0.85[EUR][1000 genomes]
rs12295138	0.81[EUR][1000 genomes]
rs1349583	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs1452047	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs1452048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17081	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs17279635	0.87[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs1839910	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898947	0.88[EUR][1000 genomes]
rs4910865	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4910866	0.85[EUR][1000 genomes]
rs4910868	0.88[EUR][1000 genomes]
rs4910869	0.87[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs6578421	0.80[YRI][hapmap]
rs6578424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66503725	0.88[EUR][1000 genomes]
rs66596383	0.90[EUR][1000 genomes]
rs67300156	0.86[EUR][1000 genomes]
rs7102215	0.85[EUR][1000 genomes]
rs7113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7120938	0.82[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap]
rs7128762	0.85[EUR][1000 genomes]
rs7129444	0.82[GIH][hapmap]
rs720571	0.86[EUR][1000 genomes]
rs750525	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7924984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7925954	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7950153	0.84[GIH][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs963998	0.83[GIH][hapmap];0.90[TSI][hapmap]
rs995498	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11030404	STIM1	cis	lung	GTEx
rs11030404	OR51A4	cis	parietal	SCAN
rs11030404	OR51E2	cis	cerebellum	SCAN
rs11030404	ANO9	cis	parietal	SCAN
rs11030404	TRIM21	cis	cerebellum	SCAN
rs11030404	RRM1	cis	Artery Tibial	GTEx
rs11030404	CD81	cis	parietal	SCAN
rs11030404	RRM1	cis	parietal	SCAN
rs11030404	IFITM5	cis	cerebellum	SCAN
rs11030404	RRM1	cis	cerebellum	SCAN
rs11030404	FAM160A2	cis	parietal	SCAN
rs11030404	RRM1	cis	Thyroid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3961200-4002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:3970800-3988600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr11:3971400-3988400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:3972800-3988800	Weak transcription	Fetal Muscle Leg	muscle
5	chr11:3973000-3988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:3973200-3981000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr11:3973200-3982400	Weak transcription	Primary B cells from cord blood	blood
8	chr11:3973200-3984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:3973200-3993200	Weak transcription	Colon Smooth Muscle	Colon
10	chr11:3973200-4008400	Weak transcription	Fetal Lung	lung
11	chr11:3973600-3993800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:3974200-3982200	Weak transcription	Brain Anterior Caudate	brain
13	chr11:3974400-3983400	Weak transcription	Small Intestine	intestine
14	chr11:3974800-3988200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr11:3974800-3988800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:3975000-4006000	Weak transcription	Right Ventricle	heart
17	chr11:3975600-3988600	Weak transcription	Dnd41	blood
18	chr11:3975600-3988800	Weak transcription	Aorta	Aorta
19	chr11:3975800-3984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:3975800-3988800	Weak transcription	Esophagus	oesophagus
21	chr11:3977200-3982200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:3977400-3983000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:3977400-3985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:3977400-3988600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:3977800-3981400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr11:3977800-3982200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:3979000-3981200	Enhancers	Placenta	Placenta
28	chr11:3979400-3981000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr11:3979400-3981800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:3979400-3982000	Enhancers	NHEK	skin
31	chr11:3979400-3982600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr11:3979400-3982600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr11:3979400-3983400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr11:3979600-3981200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:3979600-3981200	Enhancers	Thymus	Thymus
36	chr11:3979600-3981600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:3979600-3981800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr11:3979600-3981800	Enhancers	Osteobl	bone
39	chr11:3979600-3982400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr11:3979600-3982600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:3979600-3982600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr11:3979600-3982600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:3979600-3982600	Enhancers	HMEC	breast
44	chr11:3979600-3982800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr11:3979600-3982800	Enhancers	NHDF-Ad	bronchial
46	chr11:3979800-3981200	Enhancers	Psoas Muscle	Psoas
47	chr11:3979800-3982600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr11:3979800-3982600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr11:3980000-3982000	Enhancers	Liver	Liver
50	chr11:3980200-3981200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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