Variant report

Variant	rs11250129
Chromosome Location	chr8:11202154-11202155
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	USF2	chr8:11202128-11202326	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:11200246..11202306-chr8:11227732..11229716,2	K562	blood:
2	chr8:11200722..11203684-chr8:11734586..11737466,2	K562	blood:
3	chr8:11193886..11197724-chr8:11199871..11205497,8	K562	blood:

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

Extended variants
information (count: 83 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10096194	0.88[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10098322	0.84[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10110557	0.84[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10503421	0.88[CEU][hapmap]
rs11774673	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11781375	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11782706	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11784458	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784544	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11991153	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11994376	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13248147	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13250270	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13253016	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13263127	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13266233	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1435273	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17741537	0.88[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17797894	0.88[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1962656	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2060456	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]
rs2060457	0.84[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2060459	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]
rs2060465	0.84[GIH][hapmap]
rs2164272	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs2164273	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs2293855	0.87[GIH][hapmap];0.83[MEX][hapmap]
rs2293856	0.82[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap]
rs2293858	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2293859	0.84[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2293860	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2572371	0.81[CEU][hapmap]
rs2736277	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3174048	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34237267	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35631424	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35687566	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35747588	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779891	0.88[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3808513	0.84[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs3808518	0.87[GIH][hapmap]
rs4394351	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4413734	0.88[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5029571	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]
rs58283816	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62488721	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6601578	0.83[MEX][hapmap]
rs6601580	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6985146	0.84[GIH][hapmap];0.87[MEX][hapmap]
rs6985460	0.84[GIH][hapmap];0.87[MEX][hapmap]
rs6988922	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6990563	0.81[EUR][1000 genomes]
rs6995404	0.82[ASW][hapmap];0.84[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6996368	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7005469	0.92[CEU][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7008205	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7016671	0.84[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7815463	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7815802	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7815804	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7816601	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7816636	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7817658	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7819395	0.84[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7820895	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7828711	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7831346	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7833966	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7834139	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7838897	0.84[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7839053	0.84[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[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
rs11250129	DEFB134	cis	cerebellum	SCAN
rs11250129	FLJ10661	cis	cerebellum	SCAN
rs11250129	MTMR9	Cis_1M	lymphoblastoid	RTeQTL
rs11250129	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs11250129	TDH	cis	parietal	SCAN
rs11250129	TDH	cis	cerebellum	SCAN
rs11250129	C8orf48	cis	cerebellum	SCAN
rs11250129	PRSS55	cis	cerebellum	SCAN
rs11250129	C8orf79	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11194800-11204200	Weak transcription	Brain Anterior Caudate	brain
2	chr8:11195400-11202800	Weak transcription	K562	blood
3	chr8:11202000-11202200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
4	chr8:11202000-11202800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

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