Variant report

Variant	rs904009
Chromosome Location	chr8:11628129-11628130
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:11625966..11628578-chr8:11704558..11706433,2	MCF-7	breast:
2	chr8:11626986..11628635-chr8:11724070..11726191,2	K562	blood:
3	chr8:11628045..11631391-chr8:11641711..11643829,4	K562	blood:
4	chr8:11625866..11628884-chr8:11724599..11727626,3	MCF-7	breast:
5	chr8:11625747..11629309-chr8:11658765..11661345,4	K562	blood:
6	chr8:11625432..11628777-chr8:11664764..11667821,4	MCF-7	breast:
7	chr8:11625967..11628744-chr8:11645697..11648212,2	MCF-7	breast:
8	chr5:42992943..42993905-chr8:11627464..11628186,2	Hela-S3	cervix:
9	chr8:11626596..11628658-chr8:11659514..11662088,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164733	Chromatin interaction
ENSG00000227203	Chromatin interaction
ENSG00000255046	Chromatin interaction
ENSG00000079459	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10101195	0.81[CEU][hapmap]
rs17754589	0.87[CEU][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1883016	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010628	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865839	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67123108	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7000800	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8191511	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8191528	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8191534	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8191649	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
13	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs904009	NEIL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11626000-11628200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr8:11626000-11628200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr8:11626000-11628200	Active TSS	Lung	lung
4	chr8:11626400-11628200	Active TSS	Rectal Smooth Muscle	rectum
5	chr8:11626400-11628200	Active TSS	HSMM	muscle
6	chr8:11626600-11628200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr8:11626600-11628200	Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr8:11626600-11628200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
9	chr8:11626600-11628200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr8:11626600-11628200	Active TSS	Brain Anterior Caudate	brain
11	chr8:11626600-11628200	Active TSS	Brain Hippocampus Middle	brain
12	chr8:11626600-11628200	Active TSS	Brain Substantia Nigra	brain
13	chr8:11626600-11628200	Active TSS	Colon Smooth Muscle	Colon
14	chr8:11626600-11628200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr8:11626600-11628200	Active TSS	Psoas Muscle	Psoas
16	chr8:11626600-11628200	Active TSS	Right Atrium	heart
17	chr8:11626600-11628200	Active TSS	HepG2	liver
18	chr8:11626600-11628400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr8:11626600-11628400	Active TSS	A549	lung
20	chr8:11626600-11628400	Active TSS	HSMMtube	muscle
21	chr8:11626800-11628200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr8:11626800-11628200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr8:11626800-11628200	Active TSS	Brain Cingulate Gyrus	brain
24	chr8:11626800-11628200	Active TSS	Fetal Kidney	kidney
25	chr8:11626800-11628200	Active TSS	Left Ventricle	heart
26	chr8:11626800-11628200	Active TSS	Ovary	ovary
27	chr8:11626800-11628200	Active TSS	Spleen	Spleen
28	chr8:11626800-11628400	Active TSS	Aorta	Aorta
29	chr8:11626800-11628400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr8:11627000-11628200	Active TSS	Colonic Mucosa	Colon
31	chr8:11627000-11628200	Active TSS	Fetal Brain Male	brain
32	chr8:11627000-11628200	Active TSS	Thymus	Thymus
33	chr8:11627000-11628800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr8:11627400-11628200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
35	chr8:11627400-11628200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr8:11627400-11628200	Flanking Active TSS	Fetal Thymus	thymus
37	chr8:11627400-11628400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr8:11627400-11628400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr8:11627400-11628400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr8:11627400-11628400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr8:11627400-11628400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr8:11627400-11628400	Flanking Active TSS	GM12878-XiMat	blood
43	chr8:11627400-11628600	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr8:11627400-11628800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr8:11627400-11628800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr8:11627400-11629000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr8:11627400-11629000	Flanking Active TSS	Dnd41	blood
48	chr8:11627600-11628200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
49	chr8:11627600-11628200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr8:11627600-11628400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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