Variant report

Variant	rs879999
Chromosome Location	chr8:96239113-96239114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10956943	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13258855	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13259182	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13263562	0.81[ASN][1000 genomes]
rs13263858	0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13270711	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13279671	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1441394	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1441395	0.81[GIH][hapmap]
rs1441396	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1530257	0.89[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs2083616	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439629	0.86[ASN][1000 genomes]
rs2439630	0.89[CHB][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2514551	0.86[ASN][1000 genomes]
rs2514552	0.89[CHB][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2514553	0.89[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2514574	0.89[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs4492337	0.89[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs4509290	0.81[GIH][hapmap]
rs4560758	0.80[ASN][1000 genomes]
rs7815255	0.94[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs7820512	0.80[ASN][1000 genomes]
rs7835921	0.89[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs876260	0.89[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs876261	0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs879997	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879998	0.98[ASN][1000 genomes]
rs894151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9297955	0.80[ASN][1000 genomes]
rs9297956	0.80[ASN][1000 genomes]
rs9649978	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv523655	chr8:96205920-96239113	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv16466	chr8:96206151-96243934	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv6315	chr8:96216465-96261671	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv465741	chr8:96221122-96247835	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv611759	chr8:96221122-96247835	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs879999	KIF18B	trans	parietal	SCAN
rs879999	C8orf37	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96219800-96251800	Enhancers	Primary B cells from peripheral blood	blood
2	chr8:96231600-96241600	Enhancers	Fetal Thymus	thymus
3	chr8:96234000-96240000	Weak transcription	Primary T cells from cord blood	blood
4	chr8:96235000-96239600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr8:96235000-96239600	Enhancers	Placenta	Placenta
6	chr8:96235000-96242200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr8:96235200-96239600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr8:96235200-96249200	Enhancers	Primary B cells from cord blood	blood
9	chr8:96235400-96239400	Enhancers	Esophagus	oesophagus
10	chr8:96235400-96239400	Enhancers	Fetal Muscle Leg	muscle
11	chr8:96235400-96240000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr8:96235600-96239200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr8:96235600-96239600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr8:96235800-96239400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr8:96235800-96240000	Enhancers	Brain Hippocampus Middle	brain
16	chr8:96236600-96239800	Enhancers	Fetal Intestine Large	intestine
17	chr8:96237200-96239800	Enhancers	Fetal Intestine Small	intestine
18	chr8:96237400-96239200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr8:96237400-96239600	Flanking Active TSS	K562	blood
20	chr8:96237600-96239600	Enhancers	Fetal Muscle Trunk	muscle
21	chr8:96237600-96239800	Enhancers	Fetal Stomach	stomach
22	chr8:96238000-96240800	Enhancers	GM12878-XiMat	blood
23	chr8:96238200-96239200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:96238200-96239600	Weak transcription	Brain Germinal Matrix	brain
25	chr8:96238200-96239600	Enhancers	Brain Substantia Nigra	brain
26	chr8:96238400-96239400	Enhancers	Fetal Brain Male	brain
27	chr8:96238400-96239600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr8:96238600-96239800	Weak transcription	Fetal Kidney	kidney
29	chr8:96238600-96241000	Enhancers	HepG2	liver
30	chr8:96238600-96242000	Weak transcription	HSMMtube	muscle
31	chr8:96238600-96244800	Weak transcription	Left Ventricle	heart
32	chr8:96238600-96246600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr8:96238800-96239200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr8:96238800-96239400	Enhancers	Spleen	Spleen
35	chr8:96238800-96239800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr8:96238800-96241000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr8:96238800-96241000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr8:96238800-96241000	Weak transcription	HMEC	breast
39	chr8:96238800-96243800	Weak transcription	Fetal Heart	heart
40	chr8:96238800-96250200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr8:96239000-96239600	Weak transcription	Thymus	Thymus
42	chr8:96239000-96240400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr8:96239000-96240400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr8:96239000-96240800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr8:96239000-96241000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr8:96239000-96241000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr8:96239000-96241000	Weak transcription	NHEK	skin
48	chr8:96239000-96241200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr8:96239000-96243000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr8:96239000-96244000	Weak transcription	Right Atrium	heart

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