Variant report

Variant	rs61973264
Chromosome Location	chr13:48614475-48614476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr13:48614269-48614571	HepG2	liver:	n/a	chr13:48614426-48614444
2	MAFK	chr13:48614259-48614586	HepG2	liver:	n/a	chr13:48614428-48614443 chr13:48614428-48614439 chr13:48614428-48614439
3	MAFK	chr13:48614294-48614515	K562	blood:	n/a	chr13:48614428-48614443 chr13:48614428-48614439 chr13:48614428-48614439
4	MAFK	chr13:48614253-48614582	HepG2	liver:	n/a	chr13:48614428-48614443 chr13:48614428-48614439 chr13:48614428-48614439
5	MAFK	chr13:48614277-48614558	IMR90	lung:	n/a	chr13:48614428-48614443 chr13:48614428-48614439 chr13:48614428-48614439

No.	Distal block	Cell Line	Cell type
1	chr13:48614408..48616060-chr13:48806634..48809108,2	K562	blood:
2	chr13:48612252..48613991-chr13:48614134..48616270,2	MCF-7	breast:
3	chr13:48612381..48615273-chr13:48617254..48619078,2	MCF-7	breast:

Variant related genes	Relation type
SUCLA2	TF binding region
ENSG00000136156	Chromatin interaction

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

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

rs_ID	r²[population]
rs1104351	0.91[AFR][1000 genomes];1.00[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	0.82[EUR][1000 genomes]
rs12869161	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327656	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359616	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	0.94[EUR][1000 genomes]
rs1752129	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886977	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998988	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1998989	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2025864	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094195	0.82[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	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2148940	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182373	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182378	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182785	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406694	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765077	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3990876	0.84[AMR][1000 genomes]
rs4427704	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4941618	0.83[AFR][1000 genomes];0.86[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	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942720	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942723	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4942724	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	0.96[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	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	0.91[AFR][1000 genomes];0.95[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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561425	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561438	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7317685	0.91[AMR][1000 genomes]
rs7323702	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7325175	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326381	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332363	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332994	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334801	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7335797	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336170	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985469	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990099	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990541	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996051	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998786	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999270	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8001032	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001509	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002482	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002847	0.93[EUR][1000 genomes]
rs840428	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840435	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840439	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9526448	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526454	0.91[AMR][1000 genomes]
rs9526455	0.91[AMR][1000 genomes]
rs9534884	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534956	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534959	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9534966	0.91[AMR][1000 genomes]
rs9562792	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567988	0.96[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	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
2	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
rs61973264	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs61973264	MED4	cis	multi-tissue	Pritchard
rs61973264	SUCLA2	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48612400-48625000	Weak transcription	Spleen	Spleen
2	chr13:48612600-48615400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr13:48612600-48616000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr13:48612600-48616000	Weak transcription	Left Ventricle	heart
5	chr13:48612600-48616000	Weak transcription	Lung	lung
6	chr13:48612600-48623000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:48612600-48624200	Weak transcription	Gastric	stomach
8	chr13:48612600-48624800	Weak transcription	Ovary	ovary
9	chr13:48612600-48631600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:48612600-48640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:48612600-48645000	Weak transcription	Stomach Mucosa	stomach
12	chr13:48612800-48614600	Weak transcription	Fetal Muscle Leg	muscle
13	chr13:48612800-48614600	Weak transcription	Fetal Stomach	stomach
14	chr13:48612800-48614800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr13:48612800-48615000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr13:48612800-48615400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:48612800-48616000	Weak transcription	Aorta	Aorta
18	chr13:48612800-48616000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr13:48612800-48620800	Weak transcription	Primary B cells from cord blood	blood
20	chr13:48612800-48622000	Weak transcription	Brain Germinal Matrix	brain
21	chr13:48612800-48622000	Weak transcription	Placenta	Placenta
22	chr13:48612800-48622200	Weak transcription	Fetal Brain Female	brain
23	chr13:48612800-48622400	Weak transcription	Brain Substantia Nigra	brain
24	chr13:48612800-48624600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr13:48612800-48624800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr13:48612800-48625000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr13:48612800-48628000	Weak transcription	Fetal Brain Male	brain
28	chr13:48612800-48640200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:48612800-48640400	Weak transcription	Psoas Muscle	Psoas
30	chr13:48613000-48615000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr13:48613000-48615000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr13:48613000-48615200	Weak transcription	Adipose Nuclei	Adipose
33	chr13:48613000-48615200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr13:48613000-48615400	Weak transcription	Brain Angular Gyrus	brain
35	chr13:48613000-48615400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr13:48613000-48615400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr13:48613000-48617600	Weak transcription	HSMMtube	muscle
38	chr13:48613000-48621800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr13:48613000-48622200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr13:48613000-48640200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr13:48613000-48640400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr13:48613200-48614600	Weak transcription	Fetal Kidney	kidney
43	chr13:48613200-48614600	Weak transcription	Thymus	Thymus
44	chr13:48613200-48615000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr13:48613200-48615200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr13:48613200-48615200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr13:48613200-48615200	Weak transcription	Liver	Liver
48	chr13:48613200-48615200	Weak transcription	Brain Hippocampus Middle	brain
49	chr13:48613200-48615200	Weak transcription	Fetal Lung	lung
50	chr13:48613200-48615400	Weak transcription	H9 Cell Line	embryonic stem cell

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