Variant report

Variant	rs17707988
Chromosome Location	chr8:10183576-10183577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr8:10183232-10183954	GM12878	blood:	n/a	n/a
2	BATF	chr8:10183378-10183683	GM12878	blood:	n/a	chr8:10183510-10183521
3	BATF	chr8:10183330-10183659	GM12878	blood:	n/a	chr8:10183510-10183521
4	FOS	chr8:10183394-10183588	MCF10A-Er-Src	breast:	n/a	chr8:10183509-10183519 chr8:10183510-10183517 chr8:10183510-10183518 chr8:10183511-10183522
5	EBF1	chr8:10183463-10183662	GM12878	blood:	n/a	n/a
6	RUNX3	chr8:10183098-10184103	GM12878	blood:	n/a	n/a
7	FOS	chr8:10183369-10183673	MCF10A-Er-Src	breast:	n/a	chr8:10183509-10183519 chr8:10183510-10183517 chr8:10183510-10183518 chr8:10183511-10183522
8	FOS	chr8:10183393-10183641	MCF10A-Er-Src	breast:	n/a	chr8:10183509-10183519 chr8:10183510-10183517 chr8:10183510-10183518 chr8:10183511-10183522

Variant related genes	Relation type
MSRA	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10087391	0.83[AMR][1000 genomes]
rs10089339	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs10090440	0.85[EUR][1000 genomes]
rs10097184	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10111917	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10112446	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10903321	1.00[CHB][hapmap]
rs11774220	1.00[CHB][hapmap]
rs11776035	1.00[CHB][hapmap]
rs11776973	1.00[CHB][hapmap]
rs11780122	1.00[CHB][hapmap]
rs11783705	1.00[CHB][hapmap]
rs12156387	1.00[CHB][hapmap]
rs13252589	1.00[CHB][hapmap]
rs13263482	1.00[CHB][hapmap]
rs13272793	1.00[CHB][hapmap]
rs1484641	1.00[CHB][hapmap]
rs17151658	1.00[CHB][hapmap]
rs17151667	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs17151675	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs17151684	1.00[CHB][hapmap]
rs17151697	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs17151699	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs17151713	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17151728	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap]
rs17151741	1.00[CHB][hapmap]
rs17151745	1.00[CHB][hapmap]
rs17151748	1.00[CHB][hapmap]
rs17151763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17151854	0.82[MEX][hapmap]
rs17690549	1.00[CHB][hapmap]
rs17693945	1.00[CHB][hapmap]
rs17694485	1.00[CHB][hapmap]
rs17707665	1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs17708090	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17708114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17708276	1.00[MEX][hapmap]
rs17747335	1.00[CHB][hapmap]
rs17750324	1.00[CHB][hapmap]
rs17751178	1.00[CHB][hapmap]
rs28587507	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28611339	0.85[EUR][1000 genomes]
rs28870492	0.85[EUR][1000 genomes]
rs4240640	1.00[CHB][hapmap]
rs4840467	1.00[CHB][hapmap]
rs4841294	1.00[CHB][hapmap]
rs4841295	1.00[CHB][hapmap]
rs4841296	1.00[CHB][hapmap]
rs4841312	1.00[CHB][hapmap]
rs4841356	1.00[CHB][hapmap]
rs55836840	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59119294	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66533014	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66666973	0.82[EUR][1000 genomes]
rs6994060	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs6997224	1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap]
rs7014570	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs73193549	0.80[AMR][1000 genomes]
rs7822745	1.00[CHB][hapmap]
rs7835507	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7835960	1.00[CHB][hapmap]
rs7840347	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1016347	chr8:10091475-10223667	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv890347	chr8:10153082-10331636	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17707988	C8orf79	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10168400-10188600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr8:10169000-10183600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr8:10176600-10191200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:10178600-10190400	Weak transcription	Primary B cells from cord blood	blood
5	chr8:10179400-10183600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:10179400-10188400	Weak transcription	Brain Hippocampus Middle	brain
7	chr8:10179400-10189600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr8:10179400-10189800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr8:10179400-10190000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr8:10179400-10190000	Weak transcription	Brain Substantia Nigra	brain
11	chr8:10179400-10190400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr8:10179400-10190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:10179400-10191200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr8:10179400-10191200	Weak transcription	Fetal Intestine Small	intestine
15	chr8:10179400-10191200	Weak transcription	Pancreas	Pancrea
16	chr8:10179400-10192000	Weak transcription	Aorta	Aorta
17	chr8:10179600-10188000	Weak transcription	Fetal Brain Female	brain
18	chr8:10179600-10188400	Weak transcription	Brain Anterior Caudate	brain
19	chr8:10179600-10190200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr8:10179800-10183600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr8:10180200-10190200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr8:10182400-10183800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr8:10182600-10190600	Weak transcription	Spleen	Spleen
24	chr8:10182600-10192000	Weak transcription	Right Ventricle	heart
25	chr8:10182800-10186800	Weak transcription	Fetal Brain Male	brain
26	chr8:10183000-10184600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr8:10183000-10185000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr8:10183200-10183600	Enhancers	GM12878-XiMat	blood
29	chr8:10183200-10184000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr8:10183200-10184000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr8:10183200-10184000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr8:10183200-10184000	Enhancers	Brain Angular Gyrus	brain
33	chr8:10183200-10184400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr8:10183400-10183600	Enhancers	Primary T cells from cord blood	blood
35	chr8:10183400-10183800	Enhancers	Brain Germinal Matrix	brain
36	chr8:10183400-10184200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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