Variant report

Variant	rs6561425
Chromosome Location	chr13:48563246-48563247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48562284..48565237-chr13:48566749..48568983,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1104351	0.86[AMR][1000 genomes];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	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327656	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359616	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	0.94[EUR][1000 genomes]
rs1752129	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998988	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1998989	0.89[EUR][1000 genomes]
rs2025864	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094195	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	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182373	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182378	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182785	0.89[EUR][1000 genomes]
rs2406694	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765077	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427704	0.86[EUR][1000 genomes]
rs4941618	0.81[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	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942723	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4942724	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	0.82[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	0.82[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	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	0.90[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	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561438	0.91[EUR][1000 genomes]
rs7323702	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7325175	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326381	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	0.90[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	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334801	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7335797	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336170	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985469	0.82[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	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996051	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998786	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999270	0.89[EUR][1000 genomes]
rs8001032	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001509	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002482	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002847	0.93[EUR][1000 genomes]
rs840428	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840435	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840439	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.94[EUR][1000 genomes]
rs9526448	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534884	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534956	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534959	0.88[EUR][1000 genomes]
rs9562792	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567988	0.82[AMR][1000 genomes];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	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
rs6561425	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs6561425	SUCLA2	cis	multi-tissue	Pritchard
rs6561425	MED4	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48514400-48574000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr13:48532200-48565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr13:48532400-48565200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr13:48534200-48573200	Weak transcription	Brain Angular Gyrus	brain
5	chr13:48534400-48574400	Weak transcription	Small Intestine	intestine
6	chr13:48535000-48564800	Weak transcription	NHLF	lung
7	chr13:48537200-48574200	Weak transcription	Colonic Mucosa	Colon
8	chr13:48537400-48574000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr13:48537400-48574400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:48538000-48567200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:48538400-48574000	Weak transcription	Hela-S3	cervix
12	chr13:48538800-48564800	Weak transcription	Brain Germinal Matrix	brain
13	chr13:48539600-48571200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr13:48540000-48574200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr13:48540800-48565000	Weak transcription	NH-A	brain
16	chr13:48542400-48564800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr13:48542400-48565200	Weak transcription	Psoas Muscle	Psoas
18	chr13:48542400-48567000	Weak transcription	Esophagus	oesophagus
19	chr13:48543000-48574400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr13:48546400-48564600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr13:48546400-48565200	Weak transcription	Pancreas	Pancrea
22	chr13:48546600-48574400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr13:48546600-48574800	Weak transcription	Spleen	Spleen
24	chr13:48546800-48564200	Weak transcription	Lung	lung
25	chr13:48546800-48564600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr13:48546800-48567000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:48546800-48567200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr13:48546800-48571600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr13:48548000-48574200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr13:48548800-48574400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr13:48549000-48565200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr13:48550200-48565200	Weak transcription	Aorta	Aorta
33	chr13:48550800-48564200	Weak transcription	Right Ventricle	heart
34	chr13:48550800-48564800	Weak transcription	NHEK	skin
35	chr13:48550800-48574200	Weak transcription	Ovary	ovary
36	chr13:48551000-48573800	Weak transcription	Fetal Heart	heart
37	chr13:48551000-48574400	Weak transcription	HSMMtube	muscle
38	chr13:48552000-48564000	Weak transcription	Brain Hippocampus Middle	brain
39	chr13:48552000-48564600	Weak transcription	HMEC	breast
40	chr13:48552000-48574000	Weak transcription	A549	lung
41	chr13:48556800-48565200	Weak transcription	K562	blood
42	chr13:48557400-48567800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr13:48557800-48571800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr13:48557800-48572400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr13:48558000-48570800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr13:48558000-48573200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr13:48558600-48571800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr13:48558800-48569000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr13:48559000-48567800	Strong transcription	HSMM	muscle
50	chr13:48559000-48571000	Strong transcription	Primary monocytes fromperipheralblood	blood

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