Variant report

Variant	rs804269
Chromosome Location	chr8:11629119-11629120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:11628045..11631391-chr8:11641711..11643829,4	K562	blood:
2	chr8:11629053..11631703-chr8:11645453..11647397,2	K562	blood:
3	chr8:11625747..11629309-chr8:11658765..11661345,4	K562	blood:
4	chr8:11629063..11631875-chr8:11664082..11667656,3	MCF-7	breast:
5	chr8:11628184..11630862-chr8:11705136..11707099,2	K562	blood:
6	chr8:11629021..11631913-chr8:11640649..11643733,4	K562	blood:

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

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10098874	1.00[JPT][hapmap]
rs1047643	1.00[JPT][hapmap]
rs17754589	1.00[JPT][hapmap]
rs17810889	0.91[CEU][hapmap]
rs2686211	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840581	1.00[JPT][hapmap]
rs804267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8191604	1.00[JPT][hapmap]
rs8191649	1.00[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs804269	NEIL2	cis	Nerve Tibial	GTEx
rs804269	NEIL2	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11628000-11629200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:11628000-11640800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr8:11628200-11629200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr8:11628200-11629200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr8:11628200-11629400	Enhancers	Fetal Brain Male	brain
6	chr8:11628400-11629200	Enhancers	Lung	lung
7	chr8:11628400-11629800	Weak transcription	Primary T cells from cord blood	blood
8	chr8:11628400-11632200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr8:11628400-11634000	Weak transcription	Aorta	Aorta
10	chr8:11628400-11635800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr8:11628400-11637000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:11628400-11640000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr8:11628400-11640600	Weak transcription	A549	lung
14	chr8:11628400-11640600	Weak transcription	NH-A	brain
15	chr8:11628400-11641200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr8:11628400-11641200	Weak transcription	Psoas Muscle	Psoas
17	chr8:11628400-11641400	Weak transcription	Esophagus	oesophagus
18	chr8:11628400-11647200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr8:11628400-11653000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr8:11628400-11656800	Weak transcription	Small Intestine	intestine
21	chr8:11628600-11629200	Enhancers	Primary B cells from peripheral blood	blood
22	chr8:11628600-11629200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr8:11628600-11629200	Enhancers	Brain Substantia Nigra	brain
24	chr8:11628600-11629200	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr8:11628600-11629400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr8:11628600-11629400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr8:11628600-11629800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr8:11628600-11629800	Enhancers	Spleen	Spleen
29	chr8:11628600-11630000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr8:11628600-11630000	Weak transcription	Fetal Brain Female	brain
31	chr8:11628600-11630200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr8:11628600-11630200	Enhancers	Adipose Nuclei	Adipose
33	chr8:11628600-11630400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr8:11628600-11630600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr8:11628600-11630600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr8:11628600-11631600	Weak transcription	Liver	Liver
37	chr8:11628600-11632200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr8:11628600-11632400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr8:11628600-11634000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr8:11628600-11634000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr8:11628600-11634200	Weak transcription	Left Ventricle	heart
42	chr8:11628600-11635400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr8:11628600-11636800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr8:11628600-11637200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr8:11628600-11638000	Weak transcription	NHEK	skin
46	chr8:11628600-11638400	Weak transcription	NHLF	lung
47	chr8:11628600-11638800	Weak transcription	HMEC	breast
48	chr8:11628600-11640600	Weak transcription	Osteobl	bone
49	chr8:11628600-11640800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr8:11628600-11641800	Weak transcription	Muscle Satellite Cultured Cells	--

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