Variant report

Variant	rs11677860
Chromosome Location	chr2:9911957-9911958
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	chr2:9911820-9911970	HVMF	connective:	n/a	n/a
2	CTCF	chr2:9911488-9912309	A549	lung:	n/a	chr2:9911548-9911558
3	REST	chr2:9911748-9912321	H1-neurons	neurons:	n/a	chr2:9911882-9911892
4	E2F4	chr2:9911927-9911972	MCF10A-Er-Src	breast:	n/a	n/a
5	REST	chr2:9911615-9912453	H1-neurons	neurons:	n/a	chr2:9911882-9911892
6	CTCF	chr2:9911775-9911994	Gliobla	brain:	n/a	n/a
7	CTCF	chr2:9911722-9912072	IMR90	lung:	n/a	n/a
8	CTCF	chr2:9911820-9911970	HRPEpiC	eye:	n/a	n/a
9	CTCF	chr2:9911820-9911970	AG09319	gingival:	n/a	n/a
10	RAD21	chr2:9911845-9912126	IMR90	lung:	n/a	n/a
11	CTCF	chr2:9911900-9912050	HFF-Myc	foreskin:	n/a	n/a
12	CTCF	chr2:9911840-9911990	AG04449	skin:	n/a	n/a
13	RAD21	chr2:9911682-9912079	SK-N-SH_RA	brain:	n/a	chr2:9911745-9911759
14	RFX5	chr2:9911088-9912721	SK-N-SH	brain:	n/a	chr2:9911953-9911961 chr2:9911953-9911970 chr2:9911951-9911966 chr2:9911954-9911969 chr2:9911954-9911969 chr2:9911955-9911964 chr2:9911954-9911969 chr2:9911952-9911966
15	ZNF384	chr2:9911763-9912124	K562	blood:	n/a	n/a
16	RFX5	chr2:9911664-9912405	IMR90	lung:	n/a	chr2:9911953-9911961 chr2:9911953-9911970 chr2:9911951-9911966 chr2:9911954-9911969 chr2:9911954-9911969 chr2:9911955-9911964 chr2:9911954-9911969 chr2:9911952-9911966
17	CTCF	chr2:9911820-9911970	BJ	skin:	n/a	n/a
18	CTCF	chr2:9911840-9911990	NHLF	lung:	n/a	n/a
19	CTCF	chr2:9911820-9911970	HPF	lung:	n/a	n/a
20	CTCF	chr2:9911820-9911970	HCPEpiC	choroid plexus:	n/a	n/a
21	SMC3	chr2:9909429-9912221	SK-N-SH	brain:	n/a	n/a
22	CTCF	chr2:9911900-9912050	A549	lung:	n/a	n/a
23	CTCF	chr2:9911779-9911960	Fibrobl	skin:	n/a	n/a
24	CTCF	chr2:9911840-9911990	A549	lung:	n/a	n/a
25	CTCF	chr2:9911757-9912014	A549	lung:	n/a	n/a
26	CTCF	chr2:9911840-9911990	AoAF	blood vessel:	n/a	n/a
27	CTCF	chr2:9911874-9911964	K562	blood:	n/a	n/a
28	CTCF	chr2:9911820-9911970	AG04450	lung:	n/a	n/a
29	RFX5	chr2:9911843-9912108	HepG2	liver:	n/a	chr2:9911953-9911961 chr2:9911953-9911970 chr2:9911951-9911966 chr2:9911954-9911969 chr2:9911954-9911969 chr2:9911955-9911964 chr2:9911954-9911969 chr2:9911952-9911966
30	CTCF	chr2:9911820-9911970	HAc	cerebellar:	n/a	n/a
31	CTCF	chr2:9911840-9911990	AG09309	skin:	n/a	n/a
32	CTCF	chr2:9911694-9911981	A549	lung:	n/a	n/a
33	CTCF	chr2:9911840-9911990	HPF	lung:	n/a	n/a
34	CTCF	chr2:9911860-9912010	AG09309	skin:	n/a	n/a
35	CTCF	chr2:9911880-9912030	HCM	heart:	n/a	n/a
36	CTCF	chr2:9911860-9912010	AG09319	gingival:	n/a	n/a
37	CTCF	chr2:9911820-9911970	AG10803	skin:	n/a	n/a
38	CTCF	chr2:9911860-9912010	HMF	breast:	n/a	n/a
39	RFX5	chr2:9911912-9912057	Hela-S3	cervix:	n/a	chr2:9911953-9911961 chr2:9911953-9911970 chr2:9911951-9911966 chr2:9911954-9911969 chr2:9911954-9911969 chr2:9911955-9911964 chr2:9911954-9911969 chr2:9911952-9911966

No.	Distal block	Cell Line	Cell type
1	chr2:9909026..9912481-chr2:10259443..10262566,4	K562	blood:
2	chr2:9910788..9914069-chr2:9915018..9918206,3	K562	blood:
3	chr2:9911818..9914700-chr2:9914893..9917161,2	K562	blood:
4	chr2:9910905..9912855-chr2:10187356..10189319,2	K562	blood:
5	chr2:9910603..9912581-chr2:9936937..9939514,2	MCF-7	breast:
6	chr2:9910191..9912681-chr2:10179231..10181515,2	K562	blood:
7	chr2:9908744..9910867-chr2:9911219..9913679,2	K562	blood:
8	chr2:9910757..9913567-chr2:10174591..10176436,2	K562	blood:
9	chr2:9910558..9913108-chr2:10185637..10189105,3	MCF-7	breast:
10	chr2:9767821..9771151-chr2:9909693..9912271,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243491	TF binding region
ENSG00000243491	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000134308	Chromatin interaction
ENSG00000260077	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10184938	0.86[ASN][1000 genomes]
rs1106144	0.86[ASN][1000 genomes]
rs11675210	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676697	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676974	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11691911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693428	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693486	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12987514	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998168	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002561	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs870119	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs870120	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv873620	chr2:9906145-9951970	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11677860	DEF8	cis	Cerebellum	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9903200-9912000	Enhancers	Fetal Intestine Large	intestine
2	chr2:9905200-9913000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr2:9906200-9912000	Enhancers	Fetal Thymus	thymus
4	chr2:9907600-9913600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:9907800-9912000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:9908000-9912200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr2:9908000-9912400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:9908000-9912600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:9908000-9915200	Enhancers	Fetal Muscle Leg	muscle
10	chr2:9908200-9912200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr2:9908200-9913600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:9908400-9912000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:9908400-9912000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr2:9908400-9912400	Enhancers	Esophagus	oesophagus
15	chr2:9908800-9912600	Enhancers	NH-A	brain
16	chr2:9909000-9912400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:9909200-9912200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:9909200-9919200	Weak transcription	Thymus	Thymus
19	chr2:9909400-9912400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:9909400-9912400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:9909600-9912600	Enhancers	Fetal Brain Male	brain
22	chr2:9909600-9915000	Enhancers	Fetal Lung	lung
23	chr2:9909800-9912400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:9909800-9912600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:9909800-9912600	Bivalent Enhancer	Fetal Stomach	stomach
26	chr2:9909800-9914400	Enhancers	HSMMtube	muscle
27	chr2:9909800-9914800	Enhancers	Placenta	Placenta
28	chr2:9910000-9912400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:9910000-9912400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr2:9910000-9912400	Enhancers	NHLF	lung
31	chr2:9910000-9912600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr2:9910400-9912200	Enhancers	A549	lung
33	chr2:9910400-9912400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:9910400-9912400	Enhancers	Adipose Nuclei	Adipose
35	chr2:9910400-9912400	Enhancers	Right Atrium	heart
36	chr2:9910400-9912800	Enhancers	NHDF-Ad	bronchial
37	chr2:9910600-9912000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:9910600-9912200	Enhancers	HMEC	breast
39	chr2:9910600-9919000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:9910800-9912200	Enhancers	Colonic Mucosa	Colon
41	chr2:9910800-9912400	Enhancers	Brain Germinal Matrix	brain
42	chr2:9910800-9915000	Enhancers	Left Ventricle	heart
43	chr2:9911000-9912000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:9911000-9912000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:9911000-9912200	Enhancers	Brain Substantia Nigra	brain
46	chr2:9911000-9912400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:9911000-9912400	Enhancers	Brain Hippocampus Middle	brain
48	chr2:9911000-9912600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:9911000-9912600	Enhancers	Osteobl	bone
50	chr2:9911000-9912800	Enhancers	Brain Angular Gyrus	brain

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