Variant report

Variant	rs9534959
Chromosome Location	chr13:48699781-48699782
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1104351	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12869161	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12874522	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1326133	0.88[EUR][1000 genomes]
rs1326137	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1327656	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1359616	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1410116	0.94[EUR][1000 genomes]
rs1752129	0.83[AMR][1000 genomes]
rs1886977	0.88[EUR][1000 genomes]
rs1927214	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1998988	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1998989	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025864	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2094190	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2094193	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2094195	0.83[EUR][1000 genomes]
rs2104481	0.83[EUR][1000 genomes]
rs2148939	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148940	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2182373	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2182378	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2182785	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406694	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2406796	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2406798	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2765077	0.83[AMR][1000 genomes]
rs3862747	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3990876	0.92[AMR][1000 genomes]
rs4427704	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4941618	0.88[EUR][1000 genomes]
rs4941620	0.84[EUR][1000 genomes]
rs4941624	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4942720	0.82[EUR][1000 genomes]
rs4942721	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4942723	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4942724	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4942732	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4942734	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4942736	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4942740	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4942746	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61973264	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61973265	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61973266	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61973307	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61973308	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61974562	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61974563	0.88[EUR][1000 genomes]
rs61974564	0.88[EUR][1000 genomes]
rs61974579	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6561414	0.83[EUR][1000 genomes]
rs6561416	0.88[EUR][1000 genomes]
rs6561421	0.88[EUR][1000 genomes]
rs6561425	0.88[EUR][1000 genomes]
rs6561426	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6561438	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7317685	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7323702	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7323821	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7324368	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7325175	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7326381	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7326418	0.83[AMR][1000 genomes]
rs7329137	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7329266	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7329615	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7332363	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7332994	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7335797	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7336170	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73481288	0.96[ASN][1000 genomes]
rs73483108	0.96[ASN][1000 genomes]
rs73483122	0.96[ASN][1000 genomes]
rs7985469	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7990099	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7990541	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7991892	0.88[EUR][1000 genomes]
rs7996051	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7996581	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7998786	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7999270	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001032	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8001509	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8002482	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8002847	0.81[EUR][1000 genomes]
rs840428	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs840429	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs840432	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs840435	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs840437	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs840439	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9316350	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9316351	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs943066	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs943067	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9526419	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9526431	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9526441	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9526448	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9526450	1.00[ASN][1000 genomes]
rs9526454	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526455	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534884	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9534956	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9534966	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562792	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9567988	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9534959	SUCLA2	cis	multi-tissue	Pritchard
rs9534959	MED4	cis	multi-tissue	Pritchard
rs9534959	MED4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48686600-48700000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:48695800-48700000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr13:48695800-48701200	Weak transcription	Fetal Intestine Small	intestine
4	chr13:48696200-48699800	Weak transcription	Fetal Kidney	kidney
5	chr13:48696200-48701200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:48696200-48701200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr13:48696400-48699800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:48696400-48699800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:48697400-48701400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:48697800-48699800	Enhancers	HepG2	liver
11	chr13:48697800-48702200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr13:48698000-48700000	Enhancers	Lung	lung
13	chr13:48698000-48700600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr13:48698000-48700800	Enhancers	Left Ventricle	heart
15	chr13:48698400-48699800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr13:48698400-48700000	Enhancers	Adipose Nuclei	Adipose
17	chr13:48698400-48700000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr13:48698600-48699800	Weak transcription	Fetal Muscle Leg	muscle
19	chr13:48698600-48700000	Weak transcription	HMEC	breast
20	chr13:48698600-48701200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr13:48698600-48701200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:48698600-48701400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr13:48698600-48701400	Weak transcription	Small Intestine	intestine
24	chr13:48698800-48699800	Weak transcription	Brain Hippocampus Middle	brain
25	chr13:48698800-48699800	Weak transcription	Fetal Lung	lung
26	chr13:48698800-48699800	Weak transcription	Stomach Mucosa	stomach
27	chr13:48698800-48700000	Weak transcription	Gastric	stomach
28	chr13:48698800-48700000	Weak transcription	Right Ventricle	heart
29	chr13:48698800-48701200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr13:48698800-48701200	Weak transcription	NHEK	skin
31	chr13:48698800-48701400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr13:48699400-48699800	Enhancers	Esophagus	oesophagus
33	chr13:48699400-48700000	Enhancers	Colon Smooth Muscle	Colon
34	chr13:48699600-48699800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr13:48699600-48700000	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr13:48699600-48700000	Enhancers	HUVEC	blood vessel
37	chr13:48699600-48700000	Enhancers	Osteobl	bone
38	chr13:48699600-48700200	Enhancers	Ovary	ovary
39	chr13:48699600-48700200	Enhancers	Right Atrium	heart
40	chr13:48699600-48700400	Enhancers	Aorta	Aorta
41	chr13:48699600-48700400	Enhancers	HSMMtube	muscle
42	chr13:48699600-48700600	Enhancers	Fetal Stomach	stomach
43	chr13:48699600-48701200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:48699600-48702000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr13:48699600-48702200	Enhancers	Rectal Smooth Muscle	rectum

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