Variant report

Variant	rs13279040
Chromosome Location	chr8:96080389-96080390
allele	A/C
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:22)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:57915678..57917429-chr8:96079112..96080847,2	MCF-7	breast:
2	chr8:96078349..96080804-chr8:96101841..96104257,3	K562	blood:
3	chr8:96071292..96073984-chr8:96078454..96081250,3	K562	blood:
4	chr8:96035647..96037410-chr8:96078050..96080664,2	K562	blood:
5	chr8:96078172..96080522-chr8:96236324..96239006,2	MCF-7	breast:
6	chr8:96079089..96080992-chr8:96128939..96131322,2	MCF-7	breast:
7	chr8:95960626..95963944-chr8:96078458..96081828,4	MCF-7	breast:
8	chr8:96077355..96081323-chr8:96161993..96165637,3	MCF-7	breast:
9	chr8:96076398..96079120-chr8:96079944..96081555,2	K562	blood:
10	chr8:96075113..96084115-chr8:96121900..96127897,13	MCF-7	breast:
11	chr17:58537718..58539624-chr8:96080020..96082836,2	MCF-7	breast:
12	chr8:96078403..96080929-chr8:96218241..96220291,2	MCF-7	breast:
13	chr8:95958396..95961086-chr8:96079770..96081416,2	MCF-7	breast:
14	chr8:96072280..96082057-chr8:96143406..96150431,26	MCF-7	breast:
15	chr8:96079167..96081297-chr8:96267070..96269403,2	MCF-7	breast:
16	chr8:96075220..96081525-chr8:96145144..96151005,16	MCF-7	breast:
17	chr8:96079160..96082761-chr8:96145231..96147675,3	K562	blood:
18	chr8:96079846..96082376-chr8:96152010..96153617,2	MCF-7	breast:
19	chr8:96079753..96081863-chr8:96250255..96253131,2	MCF-7	breast:
20	chr8:95961629..95965113-chr8:96078252..96080869,3	MCF-7	breast:
21	chr8:96077629..96090166-chr8:96105796..96116852,50	MCF-7	breast:
22	chr8:96079008..96081719-chr8:96123344..96126236,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TP53INP1-1	chr8:96079036-96081463	ENSG00000245080

No data

Variant related genes	Relation type
ENSG00000164938	Chromatin interaction
ENSG00000175895	Chromatin interaction
ENSG00000156170	Chromatin interaction
ENSG00000253878	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10086541	0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[ASN][1000 genomes]
rs10087402	0.83[GIH][hapmap]
rs10089123	0.83[GIH][hapmap]
rs10092003	0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[ASN][1000 genomes]
rs10093594	0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[ASN][1000 genomes]
rs10096455	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10097930	0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs10098197	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10098453	0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[ASN][1000 genomes]
rs10100089	0.81[ASN][1000 genomes]
rs10105437	0.87[ASN][1000 genomes]
rs10106491	0.87[ASN][1000 genomes]
rs10111154	0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs10111300	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10112230	0.87[ASN][1000 genomes]
rs10113545	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1031388	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11774085	0.81[ASN][1000 genomes]
rs11776189	0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[ASN][1000 genomes]
rs11779506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11780931	0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs11781001	0.87[ASN][1000 genomes]
rs11781040	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11781619	0.81[AFR][1000 genomes]
rs11784178	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11785698	0.83[CEU][hapmap]
rs11786380	0.81[ASN][1000 genomes]
rs11786878	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12544717	0.82[EUR][1000 genomes]
rs13261505	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs1545480	0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16917224	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16917233	0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs2340536	0.81[AFR][1000 genomes]
rs2599711	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2599713	0.87[ASN][1000 genomes]
rs2599714	0.87[ASN][1000 genomes]
rs2599715	0.87[ASN][1000 genomes]
rs2678823	0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2678829	0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs28363725	0.81[ASN][1000 genomes]
rs28378156	0.81[ASN][1000 genomes]
rs28406132	0.81[ASN][1000 genomes]
rs28419772	0.81[ASN][1000 genomes]
rs28440026	0.81[ASN][1000 genomes]
rs28477467	0.87[ASN][1000 genomes]
rs28496357	0.81[ASN][1000 genomes]
rs28616734	0.81[ASN][1000 genomes]
rs28651964	0.81[ASN][1000 genomes]
rs28712702	0.81[ASN][1000 genomes]
rs34700722	0.81[ASN][1000 genomes]
rs35518242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4323442	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs56901035	0.87[ASN][1000 genomes]
rs57925408	0.93[ASN][1000 genomes]
rs6471505	0.81[ASN][1000 genomes]
rs6651271	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6651272	0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6982086	0.83[CEU][hapmap]
rs6985880	0.81[ASN][1000 genomes]
rs6989862	0.81[ASN][1000 genomes]
rs7002090	0.83[CEU][hapmap]
rs7002940	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7008542	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs71532343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73276406	0.81[ASN][1000 genomes]
rs73276417	0.81[ASN][1000 genomes]
rs73276437	0.87[ASN][1000 genomes]
rs73276439	0.87[ASN][1000 genomes]
rs73276444	0.87[ASN][1000 genomes]
rs7812312	0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[ASN][1000 genomes]
rs7818688	0.81[ASN][1000 genomes]
rs7826196	0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[ASN][1000 genomes]
rs7832570	0.81[ASN][1000 genomes]
rs9297950	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9297951	0.96[GIH][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv891205	chr8:96062601-96115476	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
5	esv12665	chr8:96079304-96081691	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv1809201	chr8:96079879-96081568	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv1809397	chr8:96079879-96081568	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1809522	chr8:96079879-96081568	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1810707	chr8:96079879-96081568	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1811213	chr8:96079879-96081568	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1812870	chr8:96079879-96081568	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	esv1814274	chr8:96079879-96081568	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	esv1808302	chr8:96079879-96085479	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13279040	C8orf38	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96038400-96085200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr8:96062000-96083800	Weak transcription	Fetal Brain Male	brain
3	chr8:96063800-96080400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr8:96063800-96081400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr8:96068800-96082200	Weak transcription	Fetal Brain Female	brain
6	chr8:96071200-96080600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr8:96071200-96084600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr8:96071200-96085000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr8:96071600-96081200	Weak transcription	Brain Germinal Matrix	brain
10	chr8:96071600-96083000	Weak transcription	Primary B cells from cord blood	blood
11	chr8:96071600-96084200	Weak transcription	GM12878-XiMat	blood
12	chr8:96071800-96083200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr8:96071800-96084800	Weak transcription	Thymus	Thymus
14	chr8:96072400-96085000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr8:96074800-96081400	Enhancers	Stomach Mucosa	stomach
16	chr8:96075000-96080400	Weak transcription	Fetal Kidney	kidney
17	chr8:96075000-96081200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr8:96075200-96084800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr8:96076600-96081000	Enhancers	Fetal Intestine Large	intestine
20	chr8:96076800-96081200	Enhancers	Fetal Intestine Small	intestine
21	chr8:96076800-96081400	Enhancers	Placenta	Placenta
22	chr8:96077600-96084400	Weak transcription	Gastric	stomach
23	chr8:96078200-96081400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr8:96078200-96081600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr8:96078200-96081800	Enhancers	HMEC	breast
26	chr8:96078400-96081400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr8:96078600-96082000	Weak transcription	Aorta	Aorta
28	chr8:96078800-96081200	Enhancers	Duodenum Mucosa	Duodenum
29	chr8:96078800-96081200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr8:96078800-96081400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:96079200-96081800	Enhancers	NHEK	skin
32	chr8:96079400-96081400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr8:96079400-96081400	Weak transcription	HUVEC	blood vessel
34	chr8:96079400-96081800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr8:96079600-96080600	Flanking Active TSS	K562	blood
36	chr8:96079600-96080800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr8:96079600-96081200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr8:96079600-96081600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr8:96079800-96080400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr8:96079800-96080400	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr8:96079800-96080800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr8:96079800-96081000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr8:96079800-96081400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr8:96079800-96081400	Enhancers	Brain Anterior Caudate	brain
45	chr8:96079800-96081400	Enhancers	Brain Cingulate Gyrus	brain
46	chr8:96079800-96081400	Enhancers	Brain Hippocampus Middle	brain
47	chr8:96079800-96081400	Enhancers	Brain Substantia Nigra	brain
48	chr8:96079800-96083200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr8:96080000-96080400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr8:96080000-96080600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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