Variant report

Variant	rs11236077
Chromosome Location	chr11:74079475-74079476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10431176	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs10459047	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1053021	0.87[YRI][hapmap]
rs10793072	0.87[YRI][hapmap]
rs10793073	0.87[YRI][hapmap]
rs10793074	0.87[YRI][hapmap]
rs10793079	0.81[YRI][hapmap]
rs10898966	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs10898974	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10898975	1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs10898976	1.00[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10898980	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10898984	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236042	1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11236043	1.00[CEU][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs11236044	0.84[EUR][1000 genomes]
rs11236052	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11236053	1.00[CEU][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11236054	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11236060	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11236063	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11236071	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236081	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236091	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236092	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236093	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236095	0.87[ASN][1000 genomes]
rs11236096	0.83[EUR][1000 genomes]
rs12049823	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs12225215	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12225446	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1279293	0.89[ASW][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs17132964	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1944971	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs2282488	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs2509531	0.82[EUR][1000 genomes]
rs2509532	0.83[EUR][1000 genomes]
rs2887119	0.81[YRI][hapmap]
rs3132913	0.81[EUR][1000 genomes]
rs3741130	0.87[YRI][hapmap]
rs3741132	1.00[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap]
rs3741133	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs3867270	0.87[YRI][hapmap]
rs3867271	0.87[YRI][hapmap]
rs3867272	0.87[YRI][hapmap]
rs4121668	0.92[CEU][hapmap]
rs515924	0.85[CEU][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs550552	0.92[CEU][hapmap]
rs573077	0.81[EUR][1000 genomes]
rs588725	0.85[CEU][hapmap]
rs61258589	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61288268	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61902380	0.85[EUR][1000 genomes]
rs61902404	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs625532	0.91[CEU][hapmap]
rs630078	0.92[CEU][hapmap]
rs633481	0.81[EUR][1000 genomes]
rs639228	0.92[CEU][hapmap]
rs647870	0.82[EUR][1000 genomes]
rs658976	0.92[CEU][hapmap]
rs676103	0.85[CEU][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs687958	0.81[EUR][1000 genomes]
rs7117465	0.92[CEU][hapmap]
rs7924914	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7926851	0.87[YRI][hapmap]
rs7940145	0.87[YRI][hapmap]
rs7941916	0.87[YRI][hapmap]
rs7945908	0.87[YRI][hapmap]
rs7949639	0.83[CEU][hapmap]
rs7951617	1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv1049915	chr11:74052264-74126319	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11236077	PPME1	cis	cerebellum	SCAN
rs11236077	P4HA3	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74037800-74086200	Weak transcription	Brain Anterior Caudate	brain
2	chr11:74038000-74084400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr11:74038200-74082000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:74038200-74084400	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:74038400-74084400	Weak transcription	Liver	Liver
6	chr11:74038400-74086200	Weak transcription	Adipose Nuclei	Adipose
7	chr11:74042200-74081200	Weak transcription	Hela-S3	cervix
8	chr11:74049400-74080400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:74050800-74085800	Weak transcription	Colonic Mucosa	Colon
10	chr11:74068800-74094800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:74069400-74082800	Weak transcription	Fetal Kidney	kidney
12	chr11:74071000-74083000	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:74071800-74082600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:74072000-74080600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr11:74072000-74081800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr11:74072000-74083800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:74072000-74084400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:74072000-74090200	Weak transcription	Pancreas	Pancrea
19	chr11:74072000-74092200	Weak transcription	Lung	lung
20	chr11:74072000-74095800	Weak transcription	Aorta	Aorta
21	chr11:74072200-74079600	Weak transcription	Fetal Intestine Small	intestine
22	chr11:74072200-74080400	Weak transcription	Esophagus	oesophagus
23	chr11:74072200-74080400	Weak transcription	Fetal Intestine Large	intestine
24	chr11:74072200-74081800	Weak transcription	Spleen	Spleen
25	chr11:74072200-74082400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:74072200-74082600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:74072200-74082800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:74072200-74082800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:74072200-74085800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr11:74072200-74085800	Weak transcription	Ovary	ovary
31	chr11:74072200-74097000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:74072400-74087200	Weak transcription	Fetal Stomach	stomach
33	chr11:74072400-74093200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:74072400-74108000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:74072600-74083000	Weak transcription	Brain Angular Gyrus	brain
36	chr11:74072800-74098200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr11:74075400-74095000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr11:74076600-74086000	Weak transcription	Dnd41	blood
39	chr11:74076800-74085800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:74077000-74081400	Strong transcription	Thymus	Thymus
41	chr11:74077000-74086200	Strong transcription	Fetal Thymus	thymus
42	chr11:74077200-74079800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr11:74077200-74079800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr11:74077400-74079600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:74077400-74079800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:74077400-74080800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:74077400-74081200	Strong transcription	Primary T cells from cord blood	blood
48	chr11:74077400-74081800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:74077400-74081800	Strong transcription	Primary B cells from cord blood	blood
50	chr11:74077400-74081800	Strong transcription	Brain Germinal Matrix	brain

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