Variant report

Variant	rs7933787
Chromosome Location	chr11:58916038-58916039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10128605	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10128661	0.88[EUR][1000 genomes]
rs10437720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10792219	0.95[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs10792221	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896914	0.88[EUR][1000 genomes]
rs10896922	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs10896924	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs10896925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10896926	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs10896928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896929	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896930	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896931	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10896932	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896933	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10896934	0.87[EUR][1000 genomes]
rs10896935	0.84[EUR][1000 genomes]
rs10896936	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10896937	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10896938	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896947	0.89[CEU][hapmap]
rs11229798	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs11229799	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs11229800	0.94[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11229801	0.90[EUR][1000 genomes]
rs11229837	0.95[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11229840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229848	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229851	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11229852	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11229854	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11229856	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11823977	0.94[EUR][1000 genomes]
rs11825017	0.94[EUR][1000 genomes]
rs12271831	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12272113	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12274008	0.92[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12275487	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12278163	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12280068	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12283633	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12292185	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12293649	0.92[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12293695	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12362905	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12802129	0.94[EUR][1000 genomes]
rs17153379	0.94[EUR][1000 genomes]
rs17153383	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17153415	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938588	0.94[EUR][1000 genomes]
rs1938589	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1938781	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096544	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2096586	0.88[EUR][1000 genomes]
rs2096587	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2105506	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2105507	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2154628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2186380	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2282482	0.92[EUR][1000 genomes]
rs2282483	0.91[EUR][1000 genomes]
rs2839968	0.89[CEU][hapmap]
rs2849739	0.84[EUR][1000 genomes]
rs34027305	0.93[EUR][1000 genomes]
rs34239454	0.90[EUR][1000 genomes]
rs34501069	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35293773	0.90[EUR][1000 genomes]
rs3802961	0.94[EUR][1000 genomes]
rs474847	0.90[EUR][1000 genomes]
rs55657403	0.87[EUR][1000 genomes]
rs55689653	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55989038	0.86[EUR][1000 genomes]
rs56137001	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56239606	0.87[EUR][1000 genomes]
rs58722008	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61902181	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61902223	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7126078	0.94[EUR][1000 genomes]
rs7950880	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv430388	chr11:58769524-58925824	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7933787	CD5	cis	cerebellum	SCAN
rs7933787	FAM111A	cis	parietal	SCAN
rs7933787	C11orf31	cis	parietal	SCAN
rs7933787	OR5AK2	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58912800-58916400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:58912800-58919400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:58912800-58919400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:58912800-58921400	Weak transcription	Esophagus	oesophagus
5	chr11:58912800-58924000	Weak transcription	Gastric	stomach
6	chr11:58912800-58924200	Weak transcription	Aorta	Aorta
7	chr11:58912800-58925800	Weak transcription	Ovary	ovary
8	chr11:58913000-58916200	Weak transcription	Placenta	Placenta
9	chr11:58913000-58916200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:58913000-58919200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:58913000-58919400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:58913000-58919400	Weak transcription	Colonic Mucosa	Colon
13	chr11:58913000-58922000	Weak transcription	Psoas Muscle	Psoas
14	chr11:58913000-58922600	Weak transcription	Small Intestine	intestine
15	chr11:58913000-58924600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:58913000-58925800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr11:58913200-58916200	Weak transcription	Liver	Liver
18	chr11:58913200-58916600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:58913200-58916600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:58913200-58917600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr11:58913200-58918200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:58913200-58918800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr11:58913200-58919200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:58913200-58919200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:58913200-58921200	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:58913200-58922200	Weak transcription	Fetal Stomach	stomach
27	chr11:58913200-58924400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:58913200-58925600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr11:58913200-58925600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr11:58913200-58925800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:58913200-58925800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr11:58913200-58925800	Weak transcription	Brain Anterior Caudate	brain
33	chr11:58913400-58916400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr11:58913400-58916400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:58913400-58916600	Weak transcription	Fetal Kidney	kidney
36	chr11:58913400-58916800	Weak transcription	A549	lung
37	chr11:58913400-58919200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:58913400-58919400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:58913400-58919600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr11:58913400-58920400	Weak transcription	NH-A	brain
41	chr11:58913400-58922000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:58913400-58922200	Weak transcription	K562	blood
43	chr11:58913600-58922600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr11:58913800-58916200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr11:58913800-58918800	Weak transcription	Left Ventricle	heart
46	chr11:58913800-58919200	Weak transcription	Adipose Nuclei	Adipose
47	chr11:58913800-58922000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:58913800-58923800	Weak transcription	Lung	lung
49	chr11:58913800-58925800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:58914000-58916200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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