Variant report

Variant	rs61896958
Chromosome Location	chr11:3830770-3830771
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	RAD21	chr11:3830137-3831006	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr11:3830349-3830884	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr11:3830700-3830850	HRE	kidney:	n/a	n/a
4	RCOR1	chr11:3830506-3830783	HepG2	liver:	n/a	n/a
5	MXI1	chr11:3828840-3831055	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr11:3830376-3830812	A549	lung:	n/a	n/a
7	GTF2F1	chr11:3830269-3830789	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr11:3830296-3830820	MCF-7	breast:	n/a	n/a
9	MYC	chr11:3830365-3830827	K562	blood:	n/a	chr11:3830582-3830592
10	USF2	chr11:3830356-3830816	Hela-S3	cervix:	n/a	chr11:3830581-3830592
11	CTCF	chr11:3830720-3830870	HUVEC	blood vessel:	n/a	n/a
12	CTCF	chr11:3828847-3831006	SK-N-SH	brain:	n/a	chr11:3829233-3829251 chr11:3829946-3829959
13	RAD21	chr11:3830229-3830797	A549	lung:	n/a	n/a
14	USF1	chr11:3830406-3830832	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr11:3829006-3830808	A549	lung:	n/a	chr11:3830582-3830592
16	RAD21	chr11:3830188-3830937	HCT-116	colon:	n/a	n/a
17	TEAD4	chr11:3830267-3830896	K562	blood:	n/a	n/a
18	CTCF	chr11:3830331-3830770	MCF-7	breast:	n/a	n/a
19	CTCF	chr11:3830188-3830816	K562	blood:	n/a	n/a
20	MYC	chr11:3830362-3830785	K562	blood:	n/a	chr11:3830582-3830592
21	CTCF	chr11:3830720-3830870	HPF	lung:	n/a	n/a
22	CTCF	chr11:3829974-3830967	A549	lung:	n/a	n/a
23	CTCF	chr11:3830740-3830890	GM12874	blood:	n/a	n/a
24	TCF12	chr11:3829956-3830822	A549	lung:	n/a	n/a
25	MAX	chr11:3830351-3830824	K562	blood:	n/a	chr11:3830582-3830592
26	RAD21	chr11:3830020-3830828	HCT-116	colon:	n/a	n/a
27	RAD21	chr11:3830207-3830781	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:3828900..3835031-chr11:3840756..3847684,8	K562	blood:
2	chr11:3829046..3832201-chr11:3860687..3864518,3	MCF-7	breast:
3	chr11:3827764..3831807-chr11:3860648..3864124,7	K562	blood:
4	chr11:3816139..3821205-chr11:3826361..3831544,11	MCF-7	breast:
5	chr11:3829231..3830814-chr11:4115429..4117638,2	K562	blood:
6	chr11:3829786..3831602-chr11:3876105..3877704,2	K562	blood:

Variant related genes	Relation type
PGAP2	TF binding region
ENSG00000148985	Chromatin interaction
ENSG00000110713	Chromatin interaction
ENSG00000228661	Chromatin interaction
ENSG00000263421	Chromatin interaction
ENSG00000167323	Chromatin interaction
ENSG00000167325	Chromatin interaction
ENSG00000177105	Chromatin interaction

Extended variants
information (count: 46 )
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	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17191448	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276405	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276453	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910577	1.00[ASN][1000 genomes]
rs4910846	0.86[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];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896930	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896931	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896953	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896954	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896956	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896957	1.00[ASN][1000 genomes]
rs61896959	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899361	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899362	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899363	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61899392	1.00[ASN][1000 genomes]
rs61899393	1.00[ASN][1000 genomes]
rs6578414	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101788	1.00[ASN][1000 genomes]
rs72844340	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844341	0.88[AMR][1000 genomes];0.99[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:9 , 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

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3829000-3830800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr11:3829000-3830800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr11:3829000-3830800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr11:3829200-3831000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:3829800-3833400	Enhancers	Fetal Heart	heart
6	chr11:3830200-3830800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr11:3830200-3830800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:3830200-3830800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:3830200-3830800	Enhancers	Adipose Nuclei	Adipose
10	chr11:3830200-3830800	Enhancers	Pancreas	Pancrea
11	chr11:3830200-3830800	Enhancers	Stomach Mucosa	stomach
12	chr11:3830200-3831000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:3830200-3831000	Flanking Active TSS	Hela-S3	cervix
14	chr11:3830200-3831800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:3830200-3831800	Weak transcription	Brain Anterior Caudate	brain
16	chr11:3830200-3831800	Weak transcription	HSMM	muscle
17	chr11:3830200-3832400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:3830200-3832600	Enhancers	Left Ventricle	heart
19	chr11:3830200-3832800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr11:3830200-3833200	Enhancers	Right Ventricle	heart
21	chr11:3830200-3837200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:3830200-3837600	Weak transcription	Lung	lung
23	chr11:3830200-3845200	Weak transcription	Spleen	Spleen
24	chr11:3830200-3845400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:3830200-3852400	Weak transcription	Fetal Brain Male	brain
26	chr11:3830400-3830800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr11:3830400-3830800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
28	chr11:3830400-3830800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr11:3830400-3830800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr11:3830400-3830800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr11:3830400-3830800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:3830400-3830800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr11:3830400-3830800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr11:3830400-3830800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr11:3830400-3830800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr11:3830400-3830800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr11:3830400-3830800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr11:3830400-3830800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:3830400-3830800	Enhancers	Brain Angular Gyrus	brain
40	chr11:3830400-3830800	Enhancers	Duodenum Mucosa	Duodenum
41	chr11:3830400-3830800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr11:3830400-3830800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr11:3830400-3831000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:3830400-3831000	Enhancers	Primary B cells from peripheral blood	blood
45	chr11:3830400-3831000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr11:3830400-3831000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr11:3830400-3831000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:3830400-3831000	Enhancers	Liver	Liver
49	chr11:3830400-3831000	Enhancers	Brain Hippocampus Middle	brain
50	chr11:3830400-3831000	Enhancers	Brain Substantia Nigra	brain

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