Variant report

Variant	rs11020388
Chromosome Location	chr11:93240847-93240848
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93239199..93241218-chr11:93245473..93247114,2	K562	blood:
2	chr11:93239503..93241482-chr11:93273372..93276296,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10831050	0.88[CHB][hapmap]
rs10831051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11020380	0.88[CHB][hapmap]
rs11020385	0.86[CHB][hapmap]
rs11020387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11020390	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11020391	0.88[CHB][hapmap]
rs11020394	0.91[ASN][1000 genomes]
rs11020402	0.88[CHB][hapmap]
rs11603107	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11603540	0.86[EUR][1000 genomes]
rs11603560	1.00[CEU][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs11604399	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11606253	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11606261	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11606262	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11606505	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607585	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12789912	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12790221	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12791489	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12795164	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12796609	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12806700	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs12808921	0.97[EUR][1000 genomes]
rs2305660	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2305661	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2605603	0.84[CHD][hapmap]
rs28638787	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3207348	0.80[EUR][1000 genomes]
rs34028949	0.94[EUR][1000 genomes]
rs34580908	0.97[EUR][1000 genomes]
rs34716358	0.80[EUR][1000 genomes]
rs34819559	0.93[EUR][1000 genomes]
rs34825570	0.80[EUR][1000 genomes]
rs35061570	0.80[EUR][1000 genomes]
rs35364744	0.97[EUR][1000 genomes]
rs35368196	0.93[EUR][1000 genomes]
rs35423935	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35548120	0.80[EUR][1000 genomes]
rs35901746	0.90[EUR][1000 genomes]
rs35930354	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3793999	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3794002	1.00[CEU][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3794007	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3794008	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs58462328	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6483248	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6483249	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66464546	0.80[EUR][1000 genomes]
rs67927069	0.80[EUR][1000 genomes]
rs7111773	0.94[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7130465	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71480681	0.87[EUR][1000 genomes]
rs71480682	0.97[EUR][1000 genomes]
rs71480685	0.88[EUR][1000 genomes]
rs7928401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933953	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7945684	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs897555	1.00[CEU][hapmap]

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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2760208	chr11:93172673-93266594	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv516461	chr11:93231476-93240847	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11020388	C11orf75	cis	lymphoblastoid	seeQTL
rs11020388	SMCO4	cis	Whole Blood	GTEx
rs11020388	FN5	cis	multi-tissue	Pritchard

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93211000-93253400	Weak transcription	Primary T cells from cord blood	blood
2	chr11:93211600-93243800	Weak transcription	Fetal Thymus	thymus
3	chr11:93218600-93254400	Weak transcription	Hela-S3	cervix
4	chr11:93218800-93245800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr11:93223000-93242800	Weak transcription	Adipose Nuclei	Adipose
6	chr11:93225400-93242800	Weak transcription	GM12878-XiMat	blood
7	chr11:93225600-93248800	Weak transcription	Fetal Muscle Leg	muscle
8	chr11:93226400-93257400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr11:93227000-93243800	Weak transcription	Lung	lung
10	chr11:93227200-93257600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:93228200-93243400	Weak transcription	Right Ventricle	heart
12	chr11:93228200-93248200	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:93232200-93243200	Weak transcription	Spleen	Spleen
14	chr11:93232400-93245200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:93232800-93243200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:93232800-93245800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr11:93232800-93248800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr11:93233000-93248800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:93233000-93248800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:93233000-93257400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr11:93233200-93241200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr11:93233400-93248600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:93234000-93242600	Enhancers	Liver	Liver
24	chr11:93234400-93243400	Weak transcription	Left Ventricle	heart
25	chr11:93234800-93250400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr11:93235200-93250200	Weak transcription	Aorta	Aorta
27	chr11:93235400-93243400	Weak transcription	Pancreas	Pancrea
28	chr11:93235400-93257800	Weak transcription	Gastric	stomach
29	chr11:93235600-93258800	Weak transcription	Small Intestine	intestine
30	chr11:93235800-93252600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:93236200-93243400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:93237000-93241400	Weak transcription	Fetal Intestine Small	intestine
33	chr11:93237000-93242600	Weak transcription	Dnd41	blood
34	chr11:93237000-93248800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:93238200-93241200	Weak transcription	Fetal Intestine Large	intestine
36	chr11:93238200-93242000	Weak transcription	Fetal Stomach	stomach
37	chr11:93238400-93242800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr11:93238400-93248400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:93238400-93259000	Weak transcription	Fetal Lung	lung
40	chr11:93238600-93248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:93239400-93245800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr11:93239600-93241600	Weak transcription	Fetal Brain Male	brain
43	chr11:93239600-93255600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:93240400-93242000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:93240600-93241000	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr11:93240600-93241000	Enhancers	HepG2	liver

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