Variant report

Variant	rs10835390
Chromosome Location	chr11:3981488-3981489
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	GATA3	chr11:3981181-3981501	SH-SY5Y	brain:	n/a	n/a
2	TCF7L2	chr11:3980681-3981509	HepG2	liver:	n/a	n/a
3	CEBPB	chr11:3981144-3981524	K562	blood:	n/a	chr11:3981354-3981365
4	GATA3	chr11:3981015-3981708	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr11:3980456-3981659	A549	lung:	n/a	chr11:3980760-3980769
6	CEBPB	chr11:3981160-3981534	Hela-S3	cervix:	n/a	chr11:3981354-3981365
7	CEBPB	chr11:3981059-3981548	MCF-7	breast:	n/a	chr11:3981354-3981365
8	ARID3A	chr11:3980313-3981498	HepG2	liver:	n/a	n/a
9	CEBPB	chr11:3980913-3981520	HepG2	liver:	n/a	chr11:3981354-3981365
10	CEBPB	chr11:3981208-3981512	IMR90	lung:	n/a	chr11:3981354-3981365
11	TEAD4	chr11:3980614-3981689	HepG2	liver:	n/a	n/a
12	GATA3	chr11:3981134-3981571	MCF-7	breast:	n/a	n/a
13	EP300	chr11:3980693-3981555	HepG2	liver:	n/a	n/a
14	GATA3	chr11:3981081-3981653	SK-N-SH	brain:	n/a	n/a
15	FOXA1	chr11:3980796-3981553	HepG2	liver:	n/a	n/a
16	FOXA2	chr11:3981266-3981492	HepG2	liver:	n/a	n/a
17	GATA3	chr11:3981057-3981557	MCF-7	breast:	n/a	n/a
18	CEBPB	chr11:3981182-3981524	K562	blood:	n/a	chr11:3981354-3981365

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3979407..3982038-chr11:3982601..3985547,3	K562	blood:

Variant related genes	Relation type
ENSG00000255232	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1013351	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs10500590	0.87[EUR][1000 genomes]
rs10742200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10767702	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs10767706	0.82[CHB][hapmap]
rs10767713	0.86[EUR][1000 genomes]
rs10767715	0.85[EUR][1000 genomes]
rs10767720	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10767721	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767723	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835311	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs10835312	0.83[EUR][1000 genomes]
rs10835320	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835324	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835331	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs10835333	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835340	0.86[EUR][1000 genomes]
rs10835359	0.87[EUR][1000 genomes]
rs10835399	0.87[EUR][1000 genomes]
rs10835402	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs10835403	0.86[EUR][1000 genomes]
rs10835406	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs10835407	0.87[EUR][1000 genomes]
rs11030276	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs11030404	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]
rs11030599	0.80[EUR][1000 genomes]
rs11030639	0.80[EUR][1000 genomes]
rs11493482	0.81[EUR][1000 genomes]
rs1155146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11828337	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12223176	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs12270732	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs12290747	0.85[EUR][1000 genomes]
rs12295138	0.81[EUR][1000 genomes]
rs1349583	0.87[EUR][1000 genomes]
rs1452047	0.87[EUR][1000 genomes]
rs1452048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17081	0.87[EUR][1000 genomes]
rs17279635	0.88[EUR][1000 genomes]
rs1839910	0.95[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];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898947	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs4910865	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4910866	0.85[EUR][1000 genomes]
rs4910868	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs4910869	0.82[EUR][1000 genomes]
rs6578424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs7113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7120938	0.82[CHB][hapmap]
rs7128762	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs720571	0.86[EUR][1000 genomes]
rs750525	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7924984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7925954	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7950153	0.86[EUR][1000 genomes]
rs995498	0.87[EUR][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	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
2	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
3	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
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10835390	RRM1	cis	Artery Tibial	GTEx
rs10835390	RRM1	cis	Thyroid	GTEx
rs10835390	STIM1	cis	lung	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	chr11:3973200-3982400	Weak transcription	Primary B cells from cord blood	blood
7	chr11:3973200-3984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:3973200-3993200	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:3973200-4008400	Weak transcription	Fetal Lung	lung
10	chr11:3973600-3993800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:3974200-3982200	Weak transcription	Brain Anterior Caudate	brain
12	chr11:3974400-3983400	Weak transcription	Small Intestine	intestine
13	chr11:3974800-3988200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr11:3974800-3988800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:3975000-4006000	Weak transcription	Right Ventricle	heart
16	chr11:3975600-3988600	Weak transcription	Dnd41	blood
17	chr11:3975600-3988800	Weak transcription	Aorta	Aorta
18	chr11:3975800-3984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:3975800-3988800	Weak transcription	Esophagus	oesophagus
20	chr11:3977200-3982200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:3977400-3983000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:3977400-3985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:3977400-3988600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr11:3977800-3982200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:3979400-3981800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:3979400-3982000	Enhancers	NHEK	skin
27	chr11:3979400-3982600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr11:3979400-3982600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr11:3979400-3983400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:3979600-3981600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:3979600-3981800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:3979600-3981800	Enhancers	Osteobl	bone
33	chr11:3979600-3982400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:3979600-3982600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:3979600-3982600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:3979600-3982600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:3979600-3982600	Enhancers	HMEC	breast
38	chr11:3979600-3982800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr11:3979600-3982800	Enhancers	NHDF-Ad	bronchial
40	chr11:3979800-3982600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr11:3979800-3982600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr11:3980000-3982000	Enhancers	Liver	Liver
43	chr11:3980200-3981600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:3980200-3981600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr11:3980200-3982200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:3980200-3982600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr11:3980200-3982600	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr11:3980400-3981600	Flanking Active TSS	A549	lung
49	chr11:3980400-3983400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:3980400-3984000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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