Variant report

Variant	rs6561416
Chromosome Location	chr13:48515078-48515079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1104351	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11840968	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841315	0.82[EUR][1000 genomes]
rs12869161	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327656	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359616	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	0.94[EUR][1000 genomes]
rs1752129	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886977	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998988	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1998989	0.89[EUR][1000 genomes]
rs2025864	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	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	0.89[EUR][1000 genomes]
rs2148940	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182373	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182378	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182785	0.89[EUR][1000 genomes]
rs2406694	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765077	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427704	0.86[EUR][1000 genomes]
rs4941618	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941620	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941624	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942720	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942723	0.92[EUR][1000 genomes]
rs4942724	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972210	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972223	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972227	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973264	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561414	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561425	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561438	0.91[EUR][1000 genomes]
rs7323702	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.98[EUR][1000 genomes]
rs7325175	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326381	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	0.81[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	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334801	0.90[EUR][1000 genomes]
rs7335797	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336170	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985469	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990099	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990541	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996051	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998786	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999270	0.89[EUR][1000 genomes]
rs8001032	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001509	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002482	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002847	0.93[EUR][1000 genomes]
rs840428	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840435	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840439	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.94[EUR][1000 genomes]
rs9526448	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534884	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534956	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534959	0.88[EUR][1000 genomes]
rs9562792	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567988	0.98[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6561416	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs6561416	MED4	cis	multi-tissue	Pritchard
rs6561416	SUCLA2	cis	multi-tissue	Pritchard

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	chr13:48503800-48516800	Weak transcription	NHDF-Ad	bronchial
4	chr13:48506000-48531400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr13:48506800-48522600	Weak transcription	Fetal Brain Male	brain
6	chr13:48507200-48524000	Weak transcription	Lung	lung
7	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
8	chr13:48507800-48515200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr13:48507800-48515200	Weak transcription	Osteobl	bone
10	chr13:48507800-48530600	Weak transcription	Brain Angular Gyrus	brain
11	chr13:48508000-48515200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr13:48508000-48515200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr13:48508000-48515400	Weak transcription	Fetal Kidney	kidney
14	chr13:48508000-48516200	Weak transcription	Brain Substantia Nigra	brain
15	chr13:48508000-48522400	Weak transcription	GM12878-XiMat	blood
16	chr13:48508000-48531400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr13:48508200-48515400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr13:48508200-48515800	Weak transcription	Psoas Muscle	Psoas
19	chr13:48508200-48520000	Weak transcription	HepG2	liver
20	chr13:48508200-48529600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr13:48508400-48515200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr13:48508600-48515400	Weak transcription	Brain Hippocampus Middle	brain
23	chr13:48508600-48530800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr13:48508800-48515200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr13:48508800-48522000	Weak transcription	NH-A	brain
26	chr13:48509000-48515200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr13:48509000-48530800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr13:48509200-48528400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:48509400-48515200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr13:48510200-48515400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr13:48510600-48515400	Weak transcription	Colon Smooth Muscle	Colon
32	chr13:48510800-48517400	Strong transcription	Primary T cells from cord blood	blood
33	chr13:48510800-48517400	Strong transcription	Left Ventricle	heart
34	chr13:48511000-48515200	Weak transcription	Right Ventricle	heart
35	chr13:48511000-48515400	Weak transcription	Fetal Heart	heart
36	chr13:48511000-48515400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr13:48511000-48516400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr13:48511000-48517600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr13:48511000-48530600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr13:48511000-48536600	Weak transcription	Esophagus	oesophagus
41	chr13:48511400-48516600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:48511800-48515200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr13:48511800-48516600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr13:48511800-48518800	Strong transcription	Dnd41	blood
45	chr13:48511800-48531200	Weak transcription	HUVEC	blood vessel
46	chr13:48512000-48515200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr13:48512000-48515200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr13:48512000-48516800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr13:48512000-48517600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr13:48512200-48517600	Strong transcription	Adipose Nuclei	Adipose

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