Variant report

Variant	rs55865839
Chromosome Location	chr8:11625372-11625373
allele	A/C
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	EBF1	chr8:11625359-11625531	GM12878	blood:	n/a	chr8:11625426-11625437
2	EBF1	chr8:11625205-11625542	GM12878	blood:	n/a	chr8:11625426-11625437

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11624784..11628111-chr8:11660073..11663416,4	MCF-7	breast:

Variant related genes	Relation type
NEIL2	TF binding region
ENSG00000255046	Chromatin interaction
ENSG00000079459	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1047643	1.00[ASN][1000 genomes]
rs17754589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883016	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66651545	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67123108	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7000800	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8191511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8191528	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8191534	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8191604	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8191642	0.83[AMR][1000 genomes]
rs8191649	0.84[AMR][1000 genomes]
rs904009	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised 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	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' 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 target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS 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 target site	26 gene(s)	inside rSNPs	diseases
10	nsv890360	chr8:11619163-11639991	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1023803	chr8:11623570-11721655	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv539476	chr8:11623570-11721655	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55865839	NEIL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11615800-11626800	Weak transcription	Left Ventricle	heart
2	chr8:11617000-11626800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:11617400-11626000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:11617400-11626400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr8:11617400-11626800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:11618000-11626000	Weak transcription	Pancreas	Pancrea
7	chr8:11618000-11626800	Weak transcription	Fetal Intestine Large	intestine
8	chr8:11619600-11626800	Weak transcription	Gastric	stomach
9	chr8:11620400-11626600	Weak transcription	Right Ventricle	heart
10	chr8:11621200-11626600	Weak transcription	Fetal Intestine Small	intestine
11	chr8:11622400-11626800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:11623200-11625600	Enhancers	Primary B cells from cord blood	blood
13	chr8:11623400-11625600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr8:11623400-11625600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr8:11623400-11625600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr8:11623400-11625800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr8:11623400-11625800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr8:11623400-11625800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr8:11623400-11625800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr8:11623400-11625800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr8:11623400-11626000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr8:11623400-11626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr8:11623400-11626000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr8:11623400-11626000	Weak transcription	Fetal Thymus	thymus
25	chr8:11623400-11626000	Weak transcription	Right Atrium	heart
26	chr8:11623400-11626400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr8:11623400-11626600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr8:11623400-11626600	Weak transcription	Brain Anterior Caudate	brain
29	chr8:11623400-11626600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr8:11623400-11626600	Weak transcription	Brain Substantia Nigra	brain
31	chr8:11623400-11626600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr8:11623400-11626600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr8:11623400-11626800	Weak transcription	Spleen	Spleen
34	chr8:11623600-11625600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr8:11623600-11625600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr8:11623600-11625600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr8:11623600-11625600	Weak transcription	Adipose Nuclei	Adipose
38	chr8:11623600-11625800	Weak transcription	Fetal Muscle Leg	muscle
39	chr8:11623600-11626000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr8:11623600-11626000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr8:11623600-11626000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr8:11623600-11626000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr8:11623600-11626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr8:11623600-11626000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr8:11623600-11626000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr8:11623600-11626000	Weak transcription	K562	blood
47	chr8:11623600-11626200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr8:11623600-11626400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr8:11623600-11626400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr8:11623600-11626400	Weak transcription	Primary monocytes fromperipheralblood	blood

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