Variant report

Variant	rs60729363
Chromosome Location	chr8:11647606-11647607
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:11625967..11628744-chr8:11645697..11648212,2	MCF-7	breast:
2	chr8:11625684..11627765-chr8:11645905..11648269,2	K562	blood:
3	chr8:11645433..11648215-chr8:11658187..11661640,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEIL2-1	chr8:11647514-11647895	NONHSAT125083
2	lnc-NEIL2-1	chr8:11647514-11647897	NONHSAT125082

Variant related genes	Relation type
ENSG00000154328	Chromatin interaction
ENSG00000255046	Chromatin interaction
ENSG00000079459	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10089013	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13361	1.00[AMR][1000 genomes]
rs2446	1.00[AMR][1000 genomes]
rs28380721	1.00[AMR][1000 genomes]
rs28391704	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28481870	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28615101	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28697995	0.82[AFR][1000 genomes]
rs28827548	1.00[AMR][1000 genomes]
rs3189016	1.00[AMR][1000 genomes]
rs55774923	1.00[AMR][1000 genomes]
rs55865186	1.00[AMR][1000 genomes]
rs57575026	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58057768	1.00[AMR][1000 genomes]
rs58922796	1.00[AMR][1000 genomes]
rs59270740	1.00[AMR][1000 genomes]
rs60079257	1.00[AMR][1000 genomes]
rs60409649	1.00[AMR][1000 genomes]
rs61394300	1.00[AMR][1000 genomes]
rs73543167	1.00[AMR][1000 genomes]
rs73663010	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73663017	1.00[AMR][1000 genomes]
rs73663018	1.00[AMR][1000 genomes]
rs73663020	1.00[AMR][1000 genomes]
rs73663033	1.00[AMR][1000 genomes]
rs73663036	1.00[AMR][1000 genomes]
rs8191658	0.81[AFR][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	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
11	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
12	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
13	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
14	nsv1032739	chr8:11643803-11716473	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11628400-11653000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr8:11628400-11656800	Weak transcription	Small Intestine	intestine
3	chr8:11636800-11659400	Weak transcription	Thymus	Thymus
4	chr8:11640800-11658600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr8:11641000-11658000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr8:11641000-11659600	Weak transcription	Right Atrium	heart
7	chr8:11641200-11658400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr8:11641200-11659000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr8:11641400-11648600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr8:11641600-11653600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr8:11641800-11653200	Weak transcription	Stomach Mucosa	stomach
12	chr8:11642000-11654200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:11642200-11653000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr8:11642600-11652800	Weak transcription	Colon Smooth Muscle	Colon
15	chr8:11643000-11653000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr8:11643400-11653000	Weak transcription	Fetal Kidney	kidney
17	chr8:11643400-11653000	Weak transcription	HSMM	muscle
18	chr8:11643600-11658200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr8:11643800-11653000	Weak transcription	Fetal Intestine Large	intestine
20	chr8:11643800-11653800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr8:11643800-11654000	Weak transcription	GM12878-XiMat	blood
22	chr8:11643800-11654400	Weak transcription	Gastric	stomach
23	chr8:11643800-11659400	Weak transcription	Brain Angular Gyrus	brain
24	chr8:11643800-11659600	Weak transcription	Aorta	Aorta
25	chr8:11644000-11648400	Weak transcription	Adipose Nuclei	Adipose
26	chr8:11644000-11653000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr8:11644200-11653000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr8:11644200-11653200	Weak transcription	Colonic Mucosa	Colon
29	chr8:11644200-11658400	Weak transcription	Brain Germinal Matrix	brain
30	chr8:11644400-11648200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr8:11644400-11648200	Weak transcription	A549	lung
32	chr8:11644400-11648800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr8:11644400-11653000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr8:11644400-11659400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr8:11644600-11648600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr8:11644600-11653000	Weak transcription	Placenta	Placenta
37	chr8:11644600-11654600	Weak transcription	Lung	lung
38	chr8:11644600-11654600	Weak transcription	Spleen	Spleen
39	chr8:11644600-11659400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr8:11644800-11648800	Weak transcription	Liver	Liver
41	chr8:11644800-11649400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr8:11644800-11654000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr8:11644800-11659000	Weak transcription	Primary T cells from cord blood	blood
44	chr8:11645000-11649600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr8:11645000-11650200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr8:11645000-11654000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr8:11645000-11658600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr8:11645200-11654400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr8:11645400-11648000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr8:11645600-11652800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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