Variant report

Variant	rs11138830
Chromosome Location	chr9:72085456-72085457
allele	C/T
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	SP1	chr9:72085313-72085718	A549	lung:	n/a	n/a
2	FOXA2	chr9:72085398-72085742	A549	lung:	n/a	n/a
3	FOXA2	chr9:72085295-72085906	A549	lung:	n/a	n/a
4	NR3C1	chr9:72085396-72085760	A549	lung:	n/a	n/a
5	HNF4A	chr9:72085453-72085680	HepG2	liver:	n/a	chr9:72085596-72085611 chr9:72085597-72085609 chr9:72085602-72085610 chr9:72085596-72085611 chr9:72085595-72085610 chr9:72085603-72085611

Variant related genes	Relation type
APBA1	TF binding region
ENSG00000229312	TF binding region

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10217407	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10283713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10283788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1029064	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1029065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10746594	0.85[JPT][hapmap]
rs10780360	0.82[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs10780361	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10867403	0.89[YRI][hapmap]
rs10867647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10867668	0.84[ASN][1000 genomes]
rs10867671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10867672	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10867756	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1113067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11138400	0.82[ASW][hapmap];1.00[YRI][hapmap]
rs11138419	1.00[YRI][hapmap]
rs11138581	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11138722	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11138843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11138927	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11138941	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11138980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11138986	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11139043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11139044	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11139048	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11139049	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11139050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11139160	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11139181	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11139225	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11139285	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs11788742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12235168	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12238067	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12336795	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12338371	0.84[ASN][1000 genomes]
rs12341615	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12344522	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12345500	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12347818	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12348063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12349176	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1331979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2001699	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244720	1.00[YRI][hapmap]
rs2297421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28564328	0.97[ASN][1000 genomes]
rs28769886	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34788368	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3793613	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3858105	0.81[JPT][hapmap]
rs3897966	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4323532	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4744570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4744886	0.81[JPT][hapmap]
rs4744895	0.81[ASN][1000 genomes]
rs4744901	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744902	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4744904	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap]
rs4744910	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4744911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs58898712	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61564158	0.83[ASN][1000 genomes]
rs62567192	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62567204	0.82[ASN][1000 genomes]
rs62567205	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62567206	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62567231	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62567254	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62570239	0.93[EUR][1000 genomes]
rs62570245	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6559488	0.81[JPT][hapmap]
rs6559489	0.81[JPT][hapmap]
rs6559513	0.88[YRI][hapmap]
rs6559625	0.81[CHB][hapmap]
rs7022633	0.83[ASN][1000 genomes]
rs7039417	0.88[ASN][1000 genomes]
rs7043094	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7043451	0.84[JPT][hapmap]
rs7044071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7046199	0.85[JPT][hapmap]
rs7357615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7470375	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7850384	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs885174	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[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	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
2	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1048650	chr9:72028458-72179847	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1037109	chr9:72040184-72120270	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1039966	chr9:72057304-72181564	Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv430067	chr9:72080989-72116806	Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11138830	CXCL11	trans	brain	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72046400-72085600	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:72070800-72085600	Weak transcription	Gastric	stomach
3	chr9:72077200-72086800	Weak transcription	Fetal Brain Male	brain
4	chr9:72079000-72086400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:72079000-72091600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:72079200-72086200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:72080400-72089400	Weak transcription	Fetal Thymus	thymus
8	chr9:72081200-72087000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:72081400-72085600	Weak transcription	Left Ventricle	heart
10	chr9:72081600-72090600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:72081800-72085800	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:72081800-72086200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:72082000-72091000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:72082200-72090600	Weak transcription	Fetal Lung	lung
15	chr9:72082200-72091000	Weak transcription	Fetal Stomach	stomach
16	chr9:72082400-72085600	Weak transcription	Brain Anterior Caudate	brain
17	chr9:72082400-72090200	Weak transcription	Spleen	Spleen
18	chr9:72082400-72091200	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:72082600-72086600	Weak transcription	Fetal Brain Female	brain
20	chr9:72082800-72085600	Weak transcription	Ovary	ovary
21	chr9:72082800-72085800	Weak transcription	Brain Substantia Nigra	brain
22	chr9:72082800-72088000	Enhancers	Liver	Liver
23	chr9:72082800-72091000	Weak transcription	Esophagus	oesophagus
24	chr9:72082800-72091400	Weak transcription	Brain Germinal Matrix	brain
25	chr9:72083000-72085600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:72083000-72085600	Weak transcription	Pancreas	Pancrea
27	chr9:72083000-72087800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr9:72083000-72088200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:72083000-72089800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr9:72083000-72091000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:72083200-72086200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:72083200-72087200	Weak transcription	Brain Angular Gyrus	brain
33	chr9:72084200-72085600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:72084200-72086400	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr9:72084400-72086000	Enhancers	Fetal Intestine Small	intestine
36	chr9:72084400-72086200	Enhancers	Fetal Intestine Large	intestine
37	chr9:72084400-72087000	Enhancers	Stomach Mucosa	stomach
38	chr9:72084400-72087600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr9:72084600-72085800	Weak transcription	HUVEC	blood vessel
40	chr9:72085000-72086000	Enhancers	HepG2	liver
41	chr9:72085000-72086800	Enhancers	Duodenum Mucosa	Duodenum
42	chr9:72085200-72086200	Enhancers	A549	lung
43	chr9:72085400-72086000	Strong transcription	Aorta	Aorta

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