Variant report

Variant	rs7324368
Chromosome Location	chr13:48519586-48519587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1104351	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11840968	0.80[EUR][1000 genomes]
rs11841315	0.80[EUR][1000 genomes]
rs12869161	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12874522	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1326133	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1326137	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1327656	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1359616	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1410116	0.92[EUR][1000 genomes]
rs1752129	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1886977	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1927214	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1998988	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1998989	0.87[EUR][1000 genomes]
rs2025864	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2094190	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2094193	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2094195	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2104481	0.93[EUR][1000 genomes]
rs2148939	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2148940	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2182373	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2182378	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2182785	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2406694	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2406796	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2406798	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2765077	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3862747	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4427704	0.84[EUR][1000 genomes]
rs4941618	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4941620	0.94[EUR][1000 genomes]
rs4941624	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4942720	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4942721	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4942723	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4942724	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4942732	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4942734	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4942736	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4942740	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4942746	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61972210	0.80[EUR][1000 genomes]
rs61972223	0.80[EUR][1000 genomes]
rs61972227	0.85[EUR][1000 genomes]
rs61973264	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61973265	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61973266	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61973307	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61973308	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61974562	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61974563	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61974564	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61974579	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6561414	0.93[EUR][1000 genomes]
rs6561416	0.98[EUR][1000 genomes]
rs6561421	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6561425	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6561426	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6561438	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7317685	0.83[AMR][1000 genomes]
rs7323702	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7323821	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7325175	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7326381	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7326418	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7329137	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7329266	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7329615	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7332363	0.96[EUR][1000 genomes]
rs7332994	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7334801	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7335797	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7336170	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7985469	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7990099	0.96[EUR][1000 genomes]
rs7990541	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7991892	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7996051	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7996581	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7998786	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7999270	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8001032	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8001509	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8002482	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8002847	0.91[EUR][1000 genomes]
rs840428	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs840429	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs840432	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs840435	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs840437	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs840439	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9316350	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9316351	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs943066	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs943067	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9526419	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9526431	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9526441	0.92[EUR][1000 genomes]
rs9526448	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9526454	0.83[AMR][1000 genomes]
rs9526455	0.83[AMR][1000 genomes]
rs9534884	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9534956	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9534959	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9534966	0.83[AMR][1000 genomes]
rs9562792	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9567988	0.87[AMR][1000 genomes];0.96[EUR][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
rs7324368	SUCLA2	cis	multi-tissue	Pritchard
rs7324368	MED4	cis	multi-tissue	Pritchard
rs7324368	MED4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48501000-48531200	Weak transcription	Spleen	Spleen
2	chr13:48502000-48530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:48506000-48531400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr13:48506800-48522600	Weak transcription	Fetal Brain Male	brain
5	chr13:48507200-48524000	Weak transcription	Lung	lung
6	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
7	chr13:48507800-48530600	Weak transcription	Brain Angular Gyrus	brain
8	chr13:48508000-48522400	Weak transcription	GM12878-XiMat	blood
9	chr13:48508000-48531400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr13:48508200-48520000	Weak transcription	HepG2	liver
11	chr13:48508200-48529600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:48508600-48530800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:48508800-48522000	Weak transcription	NH-A	brain
14	chr13:48509000-48530800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr13:48509200-48528400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:48511000-48530600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr13:48511000-48536600	Weak transcription	Esophagus	oesophagus
18	chr13:48511800-48531200	Weak transcription	HUVEC	blood vessel
19	chr13:48512200-48522400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr13:48512200-48530000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr13:48512200-48530800	Weak transcription	Colonic Mucosa	Colon
22	chr13:48512200-48531200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr13:48512600-48521800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr13:48512600-48522200	Weak transcription	Brain Germinal Matrix	brain
25	chr13:48512600-48527000	Weak transcription	Pancreas	Pancrea
26	chr13:48512600-48529400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr13:48512600-48530800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:48512600-48531400	Weak transcription	Aorta	Aorta
29	chr13:48512600-48537600	Weak transcription	Hela-S3	cervix
30	chr13:48512800-48522800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr13:48512800-48531200	Weak transcription	Gastric	stomach
32	chr13:48512800-48533800	Weak transcription	NHLF	lung
33	chr13:48513000-48530400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr13:48513000-48531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:48513400-48524600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr13:48513600-48530000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:48514000-48521200	Weak transcription	Small Intestine	intestine
38	chr13:48514400-48574000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr13:48515600-48522400	Weak transcription	Thymus	Thymus
40	chr13:48515600-48527000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr13:48515800-48522200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr13:48515800-48522200	Weak transcription	Osteobl	bone
43	chr13:48515800-48522800	Weak transcription	A549	lung
44	chr13:48515800-48524200	Weak transcription	HSMMtube	muscle
45	chr13:48515800-48525600	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr13:48515800-48526200	Weak transcription	Fetal Heart	heart
47	chr13:48515800-48527000	Weak transcription	Brain Hippocampus Middle	brain
48	chr13:48516000-48522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr13:48516000-48525000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr13:48516200-48531200	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links