Variant report

Variant	rs2509961
Chromosome Location	chr11:62310909-62310910
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	POLR2A	chr11:62310675-62311644	K562	blood:	n/a	n/a
2	SP1	chr11:62310039-62310947	A549	lung:	n/a	chr11:62310156-62310169 chr11:62310164-62310178 chr11:62310434-62310444
3	FOXP2	chr11:62310246-62310948	PFSK-1	brain:	n/a	n/a
4	STAT3	chr11:62310824-62310961	MCF10A-Er-Src	breast:	n/a	n/a
5	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
6	POLR2A	chr11:62310128-62311309	U87	brain:	n/a	n/a
7	CTCF	chr11:62310133-62311027	GM12878	blood:	n/a	n/a
8	CTCF	chr11:62310735-62311009	K562	blood:	n/a	n/a
9	POLR2A	chr11:62309566-62314891	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr11:62310760-62310910	GM12872	blood:	n/a	n/a
11	CTCF	chr11:62310798-62310916	Kidney_OC	kidney:	n/a	n/a
12	RAD21	chr11:62309970-62311005	A549	lung:	n/a	chr11:62310404-62310414 chr11:62310784-62310796 chr11:62310626-62310639
13	MAX	chr11:62310131-62311235	K562	blood:	n/a	chr11:62311091-62311106 chr11:62311095-62311104 chr11:62311097-62311113 chr11:62311096-62311103 chr11:62311094-62311105 chr11:62310437-62310446 chr11:62311094-62311104
14	BHLHE40	chr11:62310738-62310933	GM12878	blood:	n/a	n/a
15	CTCF	chr11:62310763-62310933	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr11:62310773-62310931	GM19239	blood:	n/a	n/a
17	POLR2A	chr11:62310861-62311030	HepG2	liver:	n/a	n/a
18	POLR2A	chr11:62309984-62315714	HUVEC	blood vessel:	n/a	n/a
19	SIN3AK20	chr11:62310673-62311164	A549	lung:	n/a	n/a
20	RAD21	chr11:62310071-62311030	IMR90	lung:	n/a	chr11:62310404-62310414 chr11:62310784-62310796 chr11:62310626-62310639
21	MYC	chr11:62310179-62310967	NB4	blood:	n/a	chr11:62310437-62310446
22	EP300	chr11:62310782-62310989	GM12878	blood:	n/a	chr11:62310899-62310906
23	POLR2A	chr11:62310557-62311110	HepG2	liver:	n/a	n/a
24	POLR2A	chr11:62309985-62314761	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr11:62309853-62314609	U87	brain:	n/a	n/a
26	CTCF	chr11:62310772-62310911	MCF-7	breast:	n/a	n/a
27	SIN3AK20	chr11:62310139-62311008	A549	lung:	n/a	n/a
28	BHLHE40	chr11:62310232-62311008	K562	blood:	n/a	chr11:62310551-62310567
29	POLR2A	chr11:62310702-62311073	A549	lung:	n/a	n/a
30	SP1	chr11:62310051-62310994	A549	lung:	n/a	chr11:62310156-62310169 chr11:62310164-62310178 chr11:62310434-62310444
31	RELA	chr11:62310053-62310937	GM18951	blood:	n/a	n/a
32	POLR2A	chr11:62310690-62311003	Gliobla	brain:	n/a	n/a
33	RAD21	chr11:62309888-62310960	H1-hESC	embryonic stem cell:	n/a	chr11:62310404-62310414 chr11:62310784-62310796 chr11:62310626-62310639
34	RAD21	chr11:62309941-62311178	HCT-116	colon:	n/a	chr11:62310404-62310414 chr11:62310784-62310796 chr11:62310626-62310639
35	SIN3AK20	chr11:62310077-62311405	PANC-1	pancreas:	n/a	n/a
36	CTCF	chr11:62310880-62311030	HRPEpiC	eye:	n/a	n/a
37	MAX	chr11:62310115-62311690	MCF-7	breast:	n/a	chr11:62311091-62311106 chr11:62311095-62311104 chr11:62311097-62311113 chr11:62311096-62311103 chr11:62311094-62311105 chr11:62310437-62310446 chr11:62311094-62311104
38	CTCF	chr11:62309847-62311112	HCT-116	colon:	n/a	chr11:62311025-62311034 chr11:62309864-62309873
39	RAD21	chr11:62309334-62311061	SK-N-SH	brain:	n/a	chr11:62310404-62310414 chr11:62310784-62310796 chr11:62310626-62310639 chr11:62309670-62309683
40	MAZ	chr11:62310097-62310957	GM12878	blood:	n/a	chr11:62310437-62310446
41	FOS	chr11:62310752-62310976	MCF10A-Er-Src	breast:	n/a	n/a
42	CTCF	chr11:62310820-62310970	SAEC	small airway:	n/a	n/a
43	POLR2A	chr11:62308122-62315675	PANC-1	pancreas:	n/a	n/a
44	CTCF	chr11:62310711-62310935	GM12878	blood:	n/a	n/a
45	MAZ	chr11:62310103-62310972	K562	blood:	n/a	chr11:62310437-62310446
46	CTCF	chr11:62310763-62310909	MCF-7	breast:	n/a	n/a
47	CTCF	chr11:62310760-62310910	GM12869	blood:	n/a	n/a
48	POLR2A	chr11:62310085-62311612	HUVEC	blood vessel:	n/a	n/a
49	SMC3	chr11:62310080-62311049	Hela-S3	cervix:	n/a	n/a
50	JUN	chr11:62309914-62311556	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62280741..62283276-chr11:62309446..62312033,2	MCF-7	breast:
2	chr11:62310191..62312888-chr11:62358804..62361545,2	MCF-7	breast:
3	chr11:62274579..62277992-chr11:62305357..62311305,7	MCF-7	breast:
4	chr11:62191888..62192838-chr11:62309887..62311003,10	K562	blood:
5	chr11:62162599..62164110-chr11:62310391..62312004,2	K562	blood:
6	chr11:62191932..62192983-chr11:62310101..62311482,6	MCF-7	breast:
7	chr11:62310407..62313306-chr11:62606623..62609508,2	MCF-7	breast:
8	chr11:62310047..62312919-chr11:62648924..62650473,2	K562	blood:
9	chr11:62310730..62313122-chr11:62436444..62438934,2	MCF-7	breast:
10	chr11:62162599..62165168-chr11:62309068..62312004,2	K562	blood:
11	chr11:62310601..62311437-chr11:62461858..62462386,2	K562	blood:
12	chr11:62196161..62199633-chr11:62307876..62311334,4	MCF-7	breast:
13	chr11:62309955..62311757-chr11:62327769..62328678,8	MCF-7	breast:
14	chr11:62263893..62266128-chr11:62309249..62311326,26	MCF-7	breast:
15	chr11:62189906..62192310-chr11:62310087..62312285,3	K562	blood:
16	chr11:62272391..62274377-chr11:62310109..62312238,2	MCF-7	breast:
17	chr11:62165780..62167539-chr11:62310095..62312002,2	K562	blood:
18	chr11:62193890..62196076-chr11:62309053..62312016,2	MCF-7	breast:
19	chr11:62263870..62269326-chr11:62305524..62310974,8	MCF-7	breast:
20	chr11:62310701..62316525-chr11:62336307..62345701,21	MCF-7	breast:
21	chr11:62201060..62204004-chr11:62310651..62312610,2	MCF-7	breast:
22	chr11:62161985..62164172-chr11:62309731..62311839,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257058	TF binding region
ENSG00000255508	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000255446	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1061093	0.84[EUR][1000 genomes]
rs11231138	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11231141	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231144	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231145	0.87[EUR][1000 genomes]
rs11231150	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs11231151	0.83[EUR][1000 genomes]
rs11231152	0.83[EUR][1000 genomes]
rs11231154	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs11231155	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11231156	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap]
rs11231161	0.92[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap]
rs11553576	0.92[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs12225213	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs17773169	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1801144	0.86[CHB][hapmap]
rs2428548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2428549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2428551	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2509962	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2509967	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2509982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2512562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2512563	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];0.97[ASN][1000 genomes]
rs2516633	0.88[CHB][hapmap];0.86[GIH][hapmap];0.91[YRI][hapmap]
rs2516634	0.81[EUR][1000 genomes]
rs2849030	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap]
rs2849031	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes]
rs35156678	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap]
rs35587183	1.00[CHB][hapmap]
rs58720921	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61296092	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7124057	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs71490390	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71490392	0.82[EUR][1000 genomes]
rs72927213	0.83[EUR][1000 genomes]
rs7928833	0.84[EUR][1000 genomes]
rs7930896	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7937146	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7942991	1.00[CHB][hapmap]
rs7943191	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2509961	SLC22A9	cis	parietal	SCAN
rs2509961	CFL1	cis	parietal	SCAN
rs2509961	C11orf48	cis	cerebellum	SCAN
rs2509961	EEF1G	cis	multi-tissue	Pritchard
rs2509961	SCYL1	cis	parietal	SCAN
rs2509961	MTA2	cis	Esophagus Mucosa	GTEx
rs2509961	TUT1	cis	parietal	SCAN
rs2509961	EML3	cis	cerebellum	SCAN
rs2509961	SLC22A25	cis	parietal	SCAN
rs2509961	EML3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62302400-62312400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:62302400-62315400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:62305600-62311200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:62305800-62311200	Transcr. at gene 5' and 3'	NHEK	skin
5	chr11:62305800-62311600	Enhancers	Pancreas	Pancrea
6	chr11:62305800-62312600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:62306400-62312200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr11:62307000-62311200	Flanking Active TSS	HMEC	breast
9	chr11:62307000-62311400	Flanking Active TSS	Osteobl	bone
10	chr11:62307000-62312200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr11:62307000-62312600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:62307000-62312600	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr11:62307000-62313600	Flanking Active TSS	GM12878-XiMat	blood
14	chr11:62308000-62311600	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr11:62308000-62313200	Transcr. at gene 5' and 3'	NHLF	lung
16	chr11:62308200-62311000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:62308200-62311200	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr11:62308200-62312200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr11:62308200-62312800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:62308200-62313000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr11:62308200-62313200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:62308400-62311200	Flanking Active TSS	Colonic Mucosa	Colon
23	chr11:62308400-62312200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:62308400-62313000	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:62308400-62313400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr11:62308600-62313200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
27	chr11:62309000-62314000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
28	chr11:62309200-62311200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:62309400-62311400	Transcr. at gene 5' and 3'	Esophagus	oesophagus
30	chr11:62309400-62312200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:62309600-62312200	Flanking Active TSS	Right Ventricle	heart
32	chr11:62309600-62312600	Flanking Active TSS	Hela-S3	cervix
33	chr11:62309600-62313200	Flanking Active TSS	Fetal Muscle Trunk	muscle
34	chr11:62309800-62311200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr11:62309800-62312000	Active TSS	Psoas Muscle	Psoas
36	chr11:62309800-62312400	Flanking Active TSS	Fetal Heart	heart
37	chr11:62309800-62312400	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr11:62309800-62313200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr11:62309800-62313400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr11:62309800-62315400	Active TSS	Aorta	Aorta
41	chr11:62310000-62311000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:62310000-62311000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
43	chr11:62310000-62311000	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr11:62310000-62311200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr11:62310000-62311200	Flanking Active TSS	Fetal Lung	lung
46	chr11:62310000-62311200	Flanking Active TSS	K562	blood
47	chr11:62310000-62311400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr11:62310000-62311400	Flanking Active TSS	Lung	lung
49	chr11:62310000-62311400	Flanking Active TSS	Stomach Mucosa	stomach
50	chr11:62310000-62311400	Flanking Active TSS	NH-A	brain

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