Variant report

Variant	rs2060459
Chromosome Location	chr8:11212599-11212600
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	SPI1	chr8:11212560-11212729	K562	blood:	n/a	chr8:11212648-11212661 chr8:11212651-11212658 chr8:11212650-11212659

No.	Distal block	Cell Line	Cell type
1	chr8:11208459..11213186-chr8:11213672..11216072,5	K562	blood:
2	chr8:11202670..11208385-chr8:11211112..11215163,10	K562	blood:
3	chr8:11210953..11213367-chr8:11221125..11223002,2	K562	blood:

Variant related genes	Relation type
TDH	TF binding region
ENSG00000255020	Chromatin interaction
ENSG00000154316	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10096194	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10098322	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs10110557	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1047950	0.82[CEU][hapmap]
rs10503421	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11250127	0.84[CEU][hapmap]
rs11250129	0.88[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11250130	0.83[ASW][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11774673	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11781375	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11781637	0.91[ASW][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11782706	0.81[EUR][1000 genomes]
rs11784458	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11784544	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11991153	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11994376	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12681987	0.89[CEU][hapmap]
rs13248147	0.82[EUR][1000 genomes]
rs13250270	0.82[EUR][1000 genomes]
rs13263127	0.81[EUR][1000 genomes]
rs13266233	0.81[EUR][1000 genomes]
rs1435273	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1435277	0.82[CEU][hapmap]
rs17741537	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17797443	0.82[CEU][hapmap]
rs17797894	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1897950	0.81[CEU][hapmap]
rs1962656	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2060456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060457	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060465	0.82[CEU][hapmap]
rs2164272	0.82[CEU][hapmap]
rs2164273	0.82[CEU][hapmap]
rs2293855	0.86[YRI][hapmap]
rs2293856	0.82[CHD][hapmap];0.85[YRI][hapmap]
rs2293858	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293859	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2293860	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2572371	0.92[CEU][hapmap]
rs2572452	0.89[CEU][hapmap]
rs2736270	0.82[CEU][hapmap]
rs2736277	0.84[CEU][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2736280	0.85[CEU][hapmap]
rs2736282	0.89[CEU][hapmap]
rs2736283	0.89[CEU][hapmap]
rs3174048	0.81[EUR][1000 genomes]
rs34237267	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35631424	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35687566	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35747588	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3779891	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs3808509	0.82[CEU][hapmap];0.86[YRI][hapmap]
rs3808513	0.82[CEU][hapmap];0.86[YRI][hapmap]
rs4394351	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4413734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4568582	0.81[CEU][hapmap]
rs5029571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58283816	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62488721	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6601578	0.86[YRI][hapmap]
rs6601580	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6601582	0.85[CEU][hapmap]
rs6985146	0.82[CEU][hapmap]
rs6985460	0.82[CEU][hapmap]
rs6988922	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6991606	0.82[CEU][hapmap];0.86[YRI][hapmap]
rs6995404	0.96[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap]
rs6996368	0.81[EUR][1000 genomes]
rs7005469	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7008205	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7016671	0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.85[YRI][hapmap]
rs7815463	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7815802	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7815804	0.84[EUR][1000 genomes]
rs7816601	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7816636	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7817658	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7819395	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7820895	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7828711	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7831346	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7833966	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7834139	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7838897	0.96[CEU][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7839053	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active 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	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	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
4	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1033312	chr8:11126800-11252170	Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv1821756	chr8:11169178-11217587	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv890354	chr8:11176147-11266131	Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv890355	chr8:11202154-11219334	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv890356	chr8:11202154-11223022	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2060459	TDH	cis	cerebellum	SCAN
rs2060459	MTMR9	Cis_1M	lymphoblastoid	RTeQTL
rs2060459	C8orf79	cis	parietal	SCAN
rs2060459	PRSS55	cis	cerebellum	SCAN
rs2060459	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs2060459	DEFB136	cis	parietal	SCAN
rs2060459	TDH	cis	parietal	SCAN
rs2060459	FLJ10661	cis	cerebellum	SCAN
rs2060459	C8orf48	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11206200-11225000	Weak transcription	Psoas Muscle	Psoas
2	chr8:11206400-11226400	Weak transcription	Brain Anterior Caudate	brain
3	chr8:11207200-11223600	Weak transcription	Brain Hippocampus Middle	brain
4	chr8:11208000-11217600	Weak transcription	Pancreas	Pancrea
5	chr8:11208000-11222400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr8:11208200-11218400	Weak transcription	A549	lung
7	chr8:11210000-11224000	Weak transcription	Brain Angular Gyrus	brain
8	chr8:11210600-11213800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr8:11212000-11212600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr8:11212200-11212600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr8:11212200-11213200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:11212200-11214200	Enhancers	K562	blood
13	chr8:11212400-11212600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr8:11212400-11219400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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