Variant report

Variant	rs61899362
Chromosome Location	chr11:3837838-3837839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:3837835-3838149	T-47D	breast:	n/a	n/a
2	NFIC	chr11:3837686-3838398	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr11:3837760-3837910	HEEpiC	esophagus:	n/a	n/a
4	POLR2A	chr11:3837736-3838265	ECC-1	luminal epithelium:	n/a	n/a
5	TEAD4	chr11:3837691-3838426	ECC-1	luminal epithelium:	n/a	n/a
6	YY1	chr11:3837831-3838291	ECC-1	luminal epithelium:	n/a	n/a
7	EP300	chr11:3837649-3838421	ECC-1	luminal epithelium:	n/a	n/a
8	NR3C1	chr11:3837834-3838188	ECC-1	luminal epithelium:	n/a	n/a
9	TEAD4	chr11:3837810-3838253	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr11:3837771-3838323	ECC-1	luminal epithelium:	n/a	n/a
11	NR3C1	chr11:3837809-3838156	ECC-1	luminal epithelium:	n/a	n/a
12	TEAD4	chr11:3837714-3838386	ECC-1	luminal epithelium:	n/a	n/a
13	SP1	chr11:3837833-3838278	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOXA1	chr11:3837789-3838152	T-47D	breast:	n/a	n/a
15	ESR1	chr11:3837805-3838121	T-47D	breast:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000250404	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1049388	1.00[ASN][1000 genomes]
rs11029983	1.00[ASN][1000 genomes]
rs11030043	1.00[ASN][1000 genomes]
rs11030044	1.00[ASN][1000 genomes]
rs11030055	1.00[ASN][1000 genomes]
rs11030173	1.00[ASN][1000 genomes]
rs11600857	1.00[ASN][1000 genomes]
rs11606318	1.00[ASN][1000 genomes]
rs11606483	1.00[ASN][1000 genomes]
rs17173882	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910577	1.00[ASN][1000 genomes]
rs4910846	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910852	1.00[ASN][1000 genomes]
rs4910856	1.00[ASN][1000 genomes]
rs4910857	1.00[ASN][1000 genomes]
rs61896929	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61896930	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896931	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896953	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896954	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896956	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896957	1.00[ASN][1000 genomes]
rs61896958	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899363	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899392	1.00[ASN][1000 genomes]
rs61899393	1.00[ASN][1000 genomes]
rs6578414	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101788	1.00[ASN][1000 genomes]
rs72844340	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844341	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73430467	1.00[ASN][1000 genomes]
rs74050940	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv1038220	chr11:3818041-3860024	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv1044882	chr11:3828986-3860024	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1044360	chr11:3832288-3860024	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3830200-3845200	Weak transcription	Spleen	Spleen
2	chr11:3830200-3845400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr11:3830200-3852400	Weak transcription	Fetal Brain Male	brain
4	chr11:3830400-3844600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:3830400-3844600	Weak transcription	Brain Germinal Matrix	brain
6	chr11:3830400-3844600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:3830400-3844600	Weak transcription	Thymus	Thymus
8	chr11:3830400-3845000	Weak transcription	Fetal Brain Female	brain
9	chr11:3830400-3846800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:3830400-3847200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:3830600-3838400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:3830600-3844600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr11:3830600-3844800	Weak transcription	NHLF	lung
14	chr11:3830600-3845000	Weak transcription	GM12878-XiMat	blood
15	chr11:3830600-3845200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:3830600-3845600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:3830600-3847000	Weak transcription	Colonic Mucosa	Colon
18	chr11:3830600-3848000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:3830600-3861000	Weak transcription	Fetal Kidney	kidney
20	chr11:3830800-3838600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:3830800-3844000	Weak transcription	Brain Angular Gyrus	brain
22	chr11:3830800-3844400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr11:3830800-3844800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr11:3830800-3845200	Weak transcription	Pancreas	Pancrea
25	chr11:3830800-3845400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr11:3830800-3845400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:3830800-3845600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr11:3830800-3845800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:3830800-3845800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr11:3830800-3846000	Weak transcription	A549	lung
31	chr11:3830800-3846200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr11:3830800-3846200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr11:3830800-3846200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:3830800-3846600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr11:3831000-3838400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr11:3831000-3842000	Weak transcription	Liver	Liver
37	chr11:3831000-3844800	Weak transcription	Dnd41	blood
38	chr11:3831000-3845400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr11:3831000-3845400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr11:3831000-3845800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr11:3831000-3845800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr11:3831000-3845800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr11:3831000-3846200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr11:3831000-3847600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:3831200-3846200	Weak transcription	Hela-S3	cervix
46	chr11:3831200-3847800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:3831400-3846200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:3831600-3846200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:3831600-3847200	Weak transcription	HepG2	liver
50	chr11:3832000-3844600	Weak transcription	Esophagus	oesophagus

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