Variant report

Variant	rs11986893
Chromosome Location	chr8:42652859-42652860
allele	A/C
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	NFYB	chr8:42652129-42652860	GM12878	blood:	n/a	chr8:42652267-42652282 chr8:42652308-42652323

Variant related genes	Relation type
CHRNA6	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10087172	0.84[JPT][hapmap];0.83[AMR][1000 genomes]
rs10092346	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10105699	0.90[ASN][1000 genomes]
rs10107450	0.90[AMR][1000 genomes]
rs10108797	0.82[AMR][1000 genomes]
rs10109040	0.91[JPT][hapmap];0.83[AMR][1000 genomes]
rs10109429	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs10110332	0.84[AMR][1000 genomes]
rs1072003	0.84[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs11995030	0.83[AMR][1000 genomes]
rs1625050	0.86[CHB][hapmap]
rs1960346	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082591	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2117225	0.83[AMR][1000 genomes]
rs2196128	0.93[ASW][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes]
rs2217732	0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs2304297	0.89[CEU][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs28501554	0.82[AMR][1000 genomes]
rs28784665	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28826992	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34996273	0.95[ASN][1000 genomes]
rs4509313	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4567031	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4737068	0.83[AMR][1000 genomes]
rs4737071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56395510	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6474418	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6474420	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6984252	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6999449	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7000412	0.81[AMR][1000 genomes]
rs7001753	0.81[AMR][1000 genomes]
rs7003968	0.92[ASN][1000 genomes]
rs7005126	0.94[ASN][1000 genomes]
rs773069	0.86[CHB][hapmap]
rs773070	0.84[CHB][hapmap]
rs773072	0.86[CHB][hapmap]
rs7812298	0.84[JPT][hapmap]
rs7825261	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7826201	0.89[ASN][1000 genomes]
rs7831096	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7835435	0.86[CHB][hapmap]
rs7841834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7845365	0.92[ASN][1000 genomes]
rs7845663	0.93[ASW][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs892413	0.85[CHD][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530880	chr8:41895241-42755506	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1034724	chr8:42386707-42772203	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	nsv428516	chr8:42577171-42731235	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
4	nsv890846	chr8:42625663-43240123	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	86 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11986893	IDO1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:42645800-42658600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr8:42647800-42660200	Weak transcription	Right Atrium	heart
3	chr8:42651600-42653000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr8:42651800-42653000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr8:42651800-42653000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr8:42651800-42655200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr8:42651800-42655400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr8:42651800-42657200	Enhancers	Primary T cells from cord blood	blood
9	chr8:42651800-42657200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr8:42652000-42655600	Enhancers	Fetal Thymus	thymus
11	chr8:42652000-42657000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr8:42652400-42653000	Active TSS	Monocytes-CD14+_RO01746	blood
13	chr8:42652400-42660600	Weak transcription	Placenta	Placenta
14	chr8:42652600-42653000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr8:42652600-42653000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr8:42652600-42653200	Enhancers	Primary B cells from peripheral blood	blood
17	chr8:42652600-42653200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr8:42652600-42653600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr8:42652800-42653200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr8:42652800-42660200	Weak transcription	Thymus	Thymus

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