Variant report

Variant	rs11231138
Chromosome Location	chr11:62316195-62316196
allele	C/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	FOXA1	chr11:62316184-62316832	HepG2	liver:	n/a	chr11:62316533-62316548
2	FOSL2	chr11:62315987-62316703	A549	lung:	n/a	n/a
3	MAX	chr11:62316156-62316754	A549	lung:	n/a	chr11:62316366-62316375
4	MAX	chr11:62309970-62316873	A549	lung:	n/a	chr11:62312136-62312143 chr11:62313404-62313414 chr11:62311091-62311106 chr11:62311095-62311104 chr11:62311097-62311113 chr11:62311096-62311103 chr11:62311094-62311105 chr11:62310437-62310446 chr11:62315029-62315039 chr11:62311094-62311104 chr11:62316366-62316375
5	FOS	chr11:62316111-62316577	HUVEC	blood vessel:	n/a	n/a
6	REST	chr11:62316113-62316722	A549	lung:	n/a	chr11:62316417-62316424 chr11:62316554-62316567
7	STAT3	chr11:62316075-62316433	MCF10A-Er-Src	breast:	n/a	chr11:62316253-62316262 chr11:62316254-62316263
8	STAT3	chr11:62315266-62316363	MCF10A-Er-Src	breast:	n/a	chr11:62315488-62315500 chr11:62316253-62316262 chr11:62316254-62316263
9	POLR2A	chr11:62316145-62316201	HepG2	liver:	n/a	n/a
10	NR3C1	chr11:62316151-62316742	A549	lung:	n/a	n/a
11	TCF12	chr11:62311919-62316972	A549	lung:	n/a	chr11:62313556-62313566 chr11:62314439-62314449 chr11:62315752-62315762
12	TCF7L2	chr11:62316169-62316734	PANC-1	pancreas:	n/a	n/a
13	MYBL2	chr11:62316178-62316813	HepG2	liver:	n/a	n/a
14	MYC	chr11:62316154-62316499	MCF10A-Er-Src	breast:	n/a	chr11:62316366-62316375
15	FOS	chr11:62315332-62316502	MCF10A-Er-Src	breast:	n/a	chr11:62315669-62315677 chr11:62315669-62315676
16	MXI1	chr11:62309801-62316378	IMR90	lung:	n/a	chr11:62311094-62311103 chr11:62311096-62311105
17	SIN3AK20	chr11:62316167-62316944	MCF-7	breast:	n/a	n/a
18	STAT3	chr11:62315310-62316510	MCF10A-Er-Src	breast:	n/a	chr11:62315488-62315500 chr11:62316253-62316262 chr11:62316254-62316263
19	ZNF263	chr11:62316028-62316363	HEK293-T-REx	kidney:	n/a	chr11:62316176-62316185
20	FOS	chr11:62316119-62316470	MCF10A-Er-Src	breast:	n/a	n/a
21	MYBL2	chr11:62316134-62316795	HepG2	liver:	n/a	n/a
22	EP300	chr11:62316142-62316786	A549	lung:	n/a	n/a
23	GATA3	chr11:62315971-62316902	A549	lung:	n/a	n/a
24	FOS	chr11:62316098-62316502	MCF10A-Er-Src	breast:	n/a	n/a
25	GATA3	chr11:62316054-62316860	MCF-7	breast:	n/a	n/a
26	FOS	chr11:62316099-62316443	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr11:62315514-62316870	K562	blood:	n/a	n/a
28	FOXA2	chr11:62315969-62317094	HepG2	liver:	n/a	n/a
29	SP1	chr11:62316088-62316754	A549	lung:	n/a	chr11:62316363-62316373 chr11:62316546-62316560
30	FOXA2	chr11:62316172-62316874	A549	lung:	n/a	n/a
31	MBD4	chr11:62316134-62316744	HepG2	liver:	n/a	n/a
32	SP1	chr11:62316046-62316878	A549	lung:	n/a	chr11:62316363-62316373 chr11:62316546-62316560

No.	Distal block	Cell Line	Cell type
1	chr11:62314813..62316842-chr11:62432248..62434823,2	K562	blood:
2	chr11:62312875..62316458-chr11:62607023..62608915,3	MCF-7	breast:
3	chr11:62314801..62317849-chr11:62431900..62434436,3	MCF-7	breast:
4	chr11:62310701..62316525-chr11:62336307..62345701,21	MCF-7	breast:

Variant related genes	Relation type
AHNAK	TF binding region
ENSG00000254772	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000214756	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1061093	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231137	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11231141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231145	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11231151	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11231152	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11231154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231155	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11231156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11231161	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11231176	1.00[JPT][hapmap]
rs11553576	0.96[CEU][hapmap]
rs12049914	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12223627	0.80[AFR][1000 genomes]
rs12225213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17773169	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1801144	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2428548	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2428549	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2428551	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2509961	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2509967	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2509982	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2512562	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2512563	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2516633	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2516634	0.85[EUR][1000 genomes]
rs2849030	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2849031	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs34894392	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35156678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs35587183	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35880596	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58720921	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60098285	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61296092	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7124057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71490390	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71490392	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71490394	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72927213	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7928833	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7930896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7937146	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7942154	0.97[ASN][1000 genomes]
rs7942991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7943191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv832180	chr11:62201605-62364828	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
5	esv3584599	chr11:62262742-62398050	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	esv1801128	chr11:62276347-62329897	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
7	esv1831183	chr11:62276347-62329897	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
9	nsv347	chr11:62297068-62338927	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11231138	EML3	cis	Esophagus Mucosa	GTEx
rs11231138	MTA2	cis	Esophagus Mucosa	GTEx
rs11231138	ROM1	cis	Thyroid	GTEx
rs11231138	EML3	cis	Whole Blood	GTEx
rs11231138	EEF1G///LOC729998	N/A	lymphoblastoid	RTeQTL
rs11231138	EEF1G	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62314600-62316200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr11:62314600-62316600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr11:62314800-62316200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:62314800-62316200	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr11:62314800-62317400	Enhancers	K562	blood
6	chr11:62314800-62319200	Weak transcription	Small Intestine	intestine
7	chr11:62314800-62320000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:62315000-62316600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:62315000-62316600	Enhancers	Placenta	Placenta
10	chr11:62315000-62316800	Enhancers	Lung	lung
11	chr11:62315000-62316800	Flanking Active TSS	A549	lung
12	chr11:62315000-62317200	Enhancers	Pancreas	Pancrea
13	chr11:62315200-62317400	Enhancers	Fetal Lung	lung
14	chr11:62315200-62317600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr11:62315200-62319000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:62315400-62316200	Enhancers	HSMMtube	muscle
17	chr11:62315400-62316600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:62315400-62316600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:62315400-62316800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:62315400-62316800	Enhancers	Fetal Stomach	stomach
21	chr11:62315400-62316800	Enhancers	Right Atrium	heart
22	chr11:62315400-62316800	Enhancers	NH-A	brain
23	chr11:62315400-62316800	Enhancers	Osteobl	bone
24	chr11:62315400-62317000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:62315400-62317000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:62315400-62317200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:62315400-62317200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:62315400-62317400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr11:62315400-62317800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:62315400-62318200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr11:62315400-62319000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:62315400-62319600	Enhancers	Ovary	ovary
33	chr11:62315400-62320400	Enhancers	Fetal Intestine Large	intestine
34	chr11:62315400-62320400	Enhancers	Fetal Intestine Small	intestine
35	chr11:62315400-62320400	Enhancers	Fetal Muscle Leg	muscle
36	chr11:62315400-62321200	Weak transcription	Gastric	stomach
37	chr11:62315400-62323600	Enhancers	Left Ventricle	heart
38	chr11:62315600-62316200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr11:62315600-62316200	Enhancers	Stomach Mucosa	stomach
40	chr11:62315600-62316200	Enhancers	HUVEC	blood vessel
41	chr11:62315600-62316400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
42	chr11:62315600-62316600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:62315600-62316600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:62315600-62316600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:62315600-62316600	Weak transcription	Aorta	Aorta
46	chr11:62315600-62316600	Enhancers	Brain Angular Gyrus	brain
47	chr11:62315600-62316600	Enhancers	HSMM	muscle
48	chr11:62315600-62316600	Enhancers	NHLF	lung
49	chr11:62315600-62316800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:62315600-62316800	Enhancers	Adipose Nuclei	Adipose

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