Variant report

Variant	rs1359616
Chromosome Location	chr13:48535289-48535290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1104351	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11840968	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841315	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12869161	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327656	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	0.94[EUR][1000 genomes]
rs1752129	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886977	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998988	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1998989	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2025864	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094195	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104481	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148939	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2148940	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182373	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182378	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182785	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406694	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765077	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3990876	0.80[AMR][1000 genomes]
rs4427704	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4941618	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941620	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941624	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942720	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942723	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4942724	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972210	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972223	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972227	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973264	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561414	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561416	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561425	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561438	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7317685	0.87[AMR][1000 genomes]
rs7323702	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7325175	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326381	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332363	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332994	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334801	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7335797	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336170	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985469	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990099	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990541	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996051	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998786	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999270	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8001032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001509	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002847	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs840428	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840435	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840439	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9526448	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526454	0.87[AMR][1000 genomes]
rs9526455	0.87[AMR][1000 genomes]
rs9534884	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534956	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534959	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9534966	0.87[AMR][1000 genomes]
rs9562792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567988	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1359616	SUCLA2	cis	multi-tissue	Pritchard
rs1359616	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs1359616	MED4	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
2	chr13:48511000-48536600	Weak transcription	Esophagus	oesophagus
3	chr13:48512600-48537600	Weak transcription	Hela-S3	cervix
4	chr13:48514400-48574000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr13:48523000-48541600	Weak transcription	Psoas Muscle	Psoas
6	chr13:48523000-48542600	Weak transcription	K562	blood
7	chr13:48523200-48536600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr13:48528000-48545800	Weak transcription	Colon Smooth Muscle	Colon
9	chr13:48528600-48541000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:48529200-48537200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr13:48529400-48537000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr13:48529400-48540200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
13	chr13:48529600-48535800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr13:48530000-48537200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr13:48530000-48538400	ZNF genes & repeats	Dnd41	blood
16	chr13:48530000-48541000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:48530000-48541200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
18	chr13:48530600-48537200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
19	chr13:48530600-48538400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
20	chr13:48530600-48538800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr13:48530600-48540200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr13:48530600-48540400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
23	chr13:48531000-48536800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr13:48531800-48536600	Weak transcription	Pancreas	Pancrea
25	chr13:48532000-48536800	Weak transcription	Colonic Mucosa	Colon
26	chr13:48532000-48540800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr13:48532000-48551400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr13:48532200-48565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr13:48532400-48536200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr13:48532400-48536400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr13:48532400-48536600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr13:48532400-48536600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr13:48532400-48536600	Weak transcription	Fetal Stomach	stomach
34	chr13:48532400-48536600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr13:48532400-48536800	Weak transcription	Lung	lung
36	chr13:48532400-48539800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:48532400-48540600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr13:48532400-48546000	Weak transcription	Aorta	Aorta
39	chr13:48532400-48559400	Weak transcription	Gastric	stomach
40	chr13:48532400-48565200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:48532600-48536800	Weak transcription	Liver	Liver
42	chr13:48532600-48545800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:48532800-48535800	Weak transcription	Osteobl	bone
44	chr13:48532800-48545800	Weak transcription	Brain Substantia Nigra	brain
45	chr13:48533200-48540600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr13:48533600-48535400	ZNF genes & repeats	Fetal Brain Female	brain
47	chr13:48533600-48536200	ZNF genes & repeats	HepG2	liver
48	chr13:48533600-48539400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr13:48533600-48540200	Strong transcription	Placenta	Placenta
50	chr13:48533800-48536000	Strong transcription	Fetal Heart	heart

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