Variant report

Variant	rs11129987
Chromosome Location	chr3:42954912-42954913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10470680	0.82[EUR][1000 genomes]
rs11129988	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1346414	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1346415	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1403525	0.82[TSI][hapmap]
rs17074894	0.83[EUR][1000 genomes]
rs1816227	0.81[EUR][1000 genomes]
rs2288371	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2288372	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2288373	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2372270	0.82[EUR][1000 genomes]
rs28378297	0.82[EUR][1000 genomes]
rs339682	1.00[CHD][hapmap]
rs339683	1.00[CHD][hapmap]
rs3915020	0.80[EUR][1000 genomes]
rs526511	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs542394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs551658	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59789275	0.87[ASN][1000 genomes]
rs60046829	0.87[ASN][1000 genomes]
rs60607395	0.87[ASN][1000 genomes]
rs60616619	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61004728	0.82[EUR][1000 genomes]
rs61102947	0.87[ASN][1000 genomes]
rs615462	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs619660	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62248962	0.81[EUR][1000 genomes]
rs62249006	0.82[EUR][1000 genomes]
rs62249007	0.82[EUR][1000 genomes]
rs62249008	0.80[EUR][1000 genomes]
rs62249009	0.82[EUR][1000 genomes]
rs62249011	0.82[EUR][1000 genomes]
rs62249013	0.80[EUR][1000 genomes]
rs638602	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs649682	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6763762	0.82[EUR][1000 genomes]
rs6773223	0.80[EUR][1000 genomes]
rs6775999	0.82[EUR][1000 genomes]
rs6778645	0.95[ASN][1000 genomes]
rs6779194	0.87[ASN][1000 genomes]
rs6798412	1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs6798520	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6865	1.00[CHD][hapmap]
rs704895	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs704899	1.00[CEU][hapmap]
rs735320	1.00[CHD][hapmap]
rs7617715	0.82[EUR][1000 genomes]
rs7621158	0.87[ASN][1000 genomes]
rs7625959	0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs7641452	1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7644923	0.81[EUR][1000 genomes]
rs834183	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs834325	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs834579	1.00[ASW][hapmap];1.00[CEU][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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs834584	1.00[ASW][hapmap];1.00[CEU][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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs834699	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9311330	0.82[EUR][1000 genomes]
rs9311331	0.82[EUR][1000 genomes]
rs9808932	0.83[EUR][1000 genomes]
rs9832875	0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs9833284	0.82[EUR][1000 genomes]
rs9852930	0.83[EUR][1000 genomes]
rs9858270	0.80[EUR][1000 genomes]
rs9874514	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv3783	chr3:42926223-42970597	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3339861	chr3:42952973-42955196	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11129987	HIGD1A	cis	cerebellum	SCAN
rs11129987	HHATL	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42948600-42955200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr3:42948600-42955600	Weak transcription	NHDF-Ad	bronchial
3	chr3:42949200-42955000	Weak transcription	Brain Substantia Nigra	brain
4	chr3:42949800-42957000	ZNF genes & repeats	Ovary	ovary
5	chr3:42951800-42959000	ZNF genes & repeats	Fetal Lung	lung
6	chr3:42952000-42955400	Strong transcription	Brain Cingulate Gyrus	brain
7	chr3:42952000-42958800	ZNF genes & repeats	Fetal Muscle Leg	muscle
8	chr3:42953000-42958800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
9	chr3:42953400-42955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:42953600-42955200	Weak transcription	Brain Angular Gyrus	brain
11	chr3:42954000-42957800	ZNF genes & repeats	Fetal Kidney	kidney
12	chr3:42954200-42955000	ZNF genes & repeats	Fetal Thymus	thymus
13	chr3:42954200-42956800	ZNF genes & repeats	Aorta	Aorta
14	chr3:42954200-42956800	ZNF genes & repeats	Esophagus	oesophagus
15	chr3:42954200-42956800	ZNF genes & repeats	Fetal Intestine Large	intestine
16	chr3:42954200-42956800	ZNF genes & repeats	Lung	lung
17	chr3:42954200-42956800	ZNF genes & repeats	Small Intestine	intestine
18	chr3:42954200-42957000	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr3:42954200-42957000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
20	chr3:42954200-42957200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
21	chr3:42954200-42957200	ZNF genes & repeats	Left Ventricle	heart
22	chr3:42954400-42955400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:42954400-42955400	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr3:42954400-42956800	ZNF genes & repeats	Placenta	Placenta
25	chr3:42954400-42956800	ZNF genes & repeats	Fetal Stomach	stomach
26	chr3:42954400-42956800	ZNF genes & repeats	Gastric	stomach
27	chr3:42954400-42957000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
28	chr3:42954400-42957000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:42954400-42957200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr3:42954400-42957200	ZNF genes & repeats	Colonic Mucosa	Colon
31	chr3:42954400-42957200	ZNF genes & repeats	Rectal Smooth Muscle	rectum
32	chr3:42954400-42957400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:42954400-42957400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:42954400-42957400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
35	chr3:42954400-42957400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
36	chr3:42954400-42957800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:42954400-42957800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:42954400-42958400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
39	chr3:42954400-42958800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
40	chr3:42954400-42959000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
41	chr3:42954400-42959200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr3:42954400-42959400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:42954400-42960200	ZNF genes & repeats	Liver	Liver
44	chr3:42954400-42960400	ZNF genes & repeats	Adipose Nuclei	Adipose
45	chr3:42954400-42960400	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr3:42954600-42955200	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr3:42954600-42955200	Strong transcription	Osteobl	bone
48	chr3:42954600-42955400	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
49	chr3:42954600-42956200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr3:42954600-42956600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood

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