Variant report

Variant	rs3850949
Chromosome Location	chr11:66153918-66153919
allele	G/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	CTCF	chr11:66153612-66154014	K562	blood:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
2	FOXA1	chr11:66153722-66153924	T-47D	breast:	n/a	n/a
3	RAD21	chr11:66153640-66154023	IMR90	lung:	n/a	chr11:66153813-66153832
4	MAZ	chr11:66153684-66153989	K562	blood:	n/a	n/a
5	CTCF	chr11:66153611-66154059	K562	blood:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
6	CUX1	chr11:66153804-66153973	GM12878	blood:	n/a	n/a
7	CTCF	chr11:66153684-66153946	GM19239	blood:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
8	RAD21	chr11:66153567-66154095	ECC-1	luminal epithelium:	n/a	chr11:66153813-66153832
9	CTCF	chr11:66153675-66153947	GM12891	blood:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
10	RAD21	chr11:66153639-66153989	SK-N-SH_RA	brain:	n/a	chr11:66153813-66153832
11	CTCF	chr11:66153581-66154110	A549	lung:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
12	ZKSCAN1	chr11:66153661-66153963	Hela-S3	cervix:	n/a	n/a
13	YY1	chr11:66153621-66153921	GM12878	blood:	n/a	n/a
14	BRCA1	chr11:66153648-66154049	Hela-S3	cervix:	n/a	n/a
15	CUX1	chr11:66153766-66154036	K562	blood:	n/a	n/a
16	CEBPB	chr11:66153565-66153918	A549	lung:	n/a	chr11:66153709-66153720
17	CTCF	chr11:66153686-66153943	LNCaP	prostate:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
18	CTCF	chr11:66153702-66153926	H1-hESC	embryonic stem cell:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
19	CTCF	chr11:66153673-66153949	Hela-S3	cervix:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
20	CTCF	chr11:66153671-66153950	MCF-7	breast:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
21	RAD21	chr11:66153525-66154216	A549	lung:	n/a	chr11:66153813-66153832
22	UBTF	chr11:66153663-66153970	K562	blood:	n/a	n/a
23	CTCF	chr11:66153688-66153937	MCF-7	breast:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
24	BHLHE40	chr11:66153787-66153982	K562	blood:	n/a	n/a
25	SMC3	chr11:66153650-66153980	HepG2	liver:	n/a	chr11:66153814-66153828
26	YY1	chr11:66153632-66153927	SK-N-SH_RA	brain:	n/a	n/a
27	JUND	chr11:66153683-66153977	K562	blood:	n/a	n/a
28	CEBPB	chr11:66153454-66154013	MCF-7	breast:	n/a	chr11:66153709-66153720
29	CEBPB	chr11:66153533-66154097	A549	lung:	n/a	chr11:66153709-66153720
30	RAD21	chr11:66153522-66154090	H1-hESC	embryonic stem cell:	n/a	chr11:66153813-66153832
31	CTCF	chr11:66153673-66153928	Kidney_OC	kidney:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
32	RCOR1	chr11:66153649-66153984	K562	blood:	n/a	n/a
33	RAD21	chr11:66153639-66154030	H1-hESC	embryonic stem cell:	n/a	chr11:66153813-66153832
34	CTCF	chr11:66153675-66153965	GM10266	blood:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
35	SMC3	chr11:66153618-66154005	GM12878	blood:	n/a	chr11:66153814-66153828
36	CTCF	chr11:66153391-66154291	SK-N-SH	brain:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
37	CTCF	chr11:66153681-66153945	HepG2	liver:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
38	CREB1	chr11:66153551-66154058	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr11:66153650-66153949	HepG2	liver:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
40	GTF2F1	chr11:66153642-66153960	Hela-S3	cervix:	n/a	n/a
41	SMC3	chr11:66153594-66154039	Hela-S3	cervix:	n/a	chr11:66153814-66153828
42	CTCF	chr11:66153668-66153986	HUVEC	blood vessel:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
43	ATF2	chr11:66153571-66154038	H1-hESC	embryonic stem cell:	n/a	n/a
44	CHD1	chr11:66153856-66154040	GM12878	blood:	n/a	n/a
45	MAZ	chr11:66153729-66153929	GM12878	blood:	n/a	n/a
46	PAX5	chr11:66153536-66153939	GM12878	blood:	n/a	n/a
47	RAD21	chr11:66153569-66154074	ECC-1	luminal epithelium:	n/a	chr11:66153813-66153832
48	GATA2	chr11:66153700-66154121	SH-SY5Y	brain:	n/a	n/a
49	CTCF	chr11:66153672-66153952	MCF-7	breast:	n/a	chr11:66153814-66153835 chr11:66153812-66153830 chr11:66153815-66153828 chr11:66153813-66153829
50	REST	chr11:66153587-66154030	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66153788..66154297-chr11:66176029..66176543,2	K562	blood:
2	chr11:66079009..66079940-chr11:66153342..66154110,2	MCF-7	breast:
3	chr11:66153350..66154299-chr11:66206205..66207048,2	K562	blood:
4	chr11:66131610..66134114-chr11:66151931..66153966,2	MCF-7	breast:
5	chr11:66139011..66141027-chr11:66151087..66154063,3	MCF-7	breast:
6	chr11:66153408..66154161-chr11:66197381..66197991,2	MCF-7	breast:
7	chr11:66152365..66155241-chr11:66220899..66223250,2	K562	blood:
8	chr11:66079417..66080029-chr11:66153138..66154277,3	MCF-7	breast:
9	chr11:66138046..66140971-chr11:66152140..66155072,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254736	TF binding region
ENSG00000174669	Chromatin interaction
ENSG00000174547	Chromatin interaction
ENSG00000254596	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1039593	1.00[EUR][1000 genomes]
rs10750785	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10750787	1.00[EUR][1000 genomes]
rs10791871	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10791875	1.00[EUR][1000 genomes]
rs10791877	1.00[EUR][1000 genomes]
rs1189692	1.00[EUR][1000 genomes]
rs1190626	1.00[TSI][hapmap]
rs1190627	1.00[EUR][1000 genomes]
rs1190628	1.00[EUR][1000 genomes]
rs1190630	1.00[EUR][1000 genomes]
rs1203483	1.00[EUR][1000 genomes]
rs12281049	1.00[ASW][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1320675	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1344410	0.93[ASW][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1532823	1.00[EUR][1000 genomes]
rs1566871	1.00[EUR][1000 genomes]
rs1621469	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1700188	1.00[EUR][1000 genomes]
rs1784030	1.00[EUR][1000 genomes]
rs1784035	1.00[EUR][1000 genomes]
rs1785623	0.93[ASW][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1785624	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1785636	1.00[EUR][1000 genomes]
rs1791677	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2292123	0.93[ASW][hapmap];0.96[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs3016763	1.00[EUR][1000 genomes]
rs3132761	1.00[EUR][1000 genomes]
rs35599411	1.00[EUR][1000 genomes]
rs3867130	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4290235	1.00[EUR][1000 genomes]
rs4930358	0.92[ASW][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4930359	1.00[ASW][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4930361	1.00[EUR][1000 genomes]
rs4930364	1.00[EUR][1000 genomes]
rs4930367	1.00[EUR][1000 genomes]
rs495264	1.00[EUR][1000 genomes]
rs525698	1.00[EUR][1000 genomes]
rs55978400	0.83[AMR][1000 genomes]
rs6421643	1.00[TSI][hapmap]
rs670900	1.00[EUR][1000 genomes]
rs7104297	0.93[ASW][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7105162	1.00[EUR][1000 genomes]
rs7111197	0.85[AFR][1000 genomes]
rs7125100	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7130857	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7131396	1.00[EUR][1000 genomes]
rs71457730	1.00[EUR][1000 genomes]
rs908693	1.00[EUR][1000 genomes]
rs948359	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66153600-66154000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr11:66153600-66154000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:66153600-66154000	Enhancers	Primary B cells from cord blood	blood
4	chr11:66153600-66154000	Flanking Active TSS	Primary B cells from peripheral blood	blood
5	chr11:66153600-66154000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr11:66153600-66154000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr11:66153600-66154000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
8	chr11:66153600-66154000	Flanking Active TSS	Brain Anterior Caudate	brain
9	chr11:66153600-66154000	Active TSS	Brain Hippocampus Middle	brain
10	chr11:66153600-66154000	Flanking Active TSS	Colonic Mucosa	Colon
11	chr11:66153600-66154000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr11:66153600-66154000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr11:66153600-66154000	Enhancers	Spleen	Spleen
14	chr11:66153600-66154200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:66153600-66154200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr11:66153600-66154200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:66153600-66154200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr11:66153600-66154200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
19	chr11:66153600-66154200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:66153600-66154200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr11:66153600-66154200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:66153600-66154200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:66153600-66154200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr11:66153600-66154200	Active TSS	Brain Angular Gyrus	brain
25	chr11:66153600-66154200	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr11:66153600-66154200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr11:66153600-66154200	Bivalent Enhancer	Fetal Brain Male	brain
28	chr11:66153600-66154200	Active TSS	Fetal Brain Female	brain
29	chr11:66153600-66154200	Bivalent Enhancer	Fetal Intestine Large	intestine
30	chr11:66153600-66154200	Enhancers	Placenta	Placenta
31	chr11:66153600-66154200	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr11:66153600-66154200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr11:66153600-66154200	Flanking Active TSS	Dnd41	blood
34	chr11:66153600-66154200	Enhancers	GM12878-XiMat	blood
35	chr11:66153600-66154200	Flanking Active TSS	Hela-S3	cervix
36	chr11:66153600-66154200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
37	chr11:66153600-66154400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:66153600-66154400	Enhancers	Esophagus	oesophagus
39	chr11:66153600-66154400	Enhancers	Fetal Thymus	thymus
40	chr11:66153800-66154000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:66153800-66154000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:66153800-66154000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr11:66153800-66154000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:66153800-66154000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
45	chr11:66153800-66154000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr11:66153800-66154000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:66153800-66154000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:66153800-66154000	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr11:66153800-66154000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:66153800-66154000	Flanking Active TSS	Colon Smooth Muscle	Colon

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