Variant report

Variant	rs7999505
Chromosome Location	chr13:48576238-48576239
allele	A/G
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	FOS	chr13:48575908-48576259	MCF10A-Er-Src	breast:	n/a	n/a
2	TFAP2C	chr13:48574861-48576517	Hela-S3	cervix:	n/a	chr13:48575177-48575192
3	TCF7L2	chr13:48575208-48576583	Hela-S3	cervix:	n/a	n/a
4	MAX	chr13:48576175-48576545	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr13:48575197-48576375	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr13:48575336-48576275	MCF10A-Er-Src	breast:	n/a	n/a
7	RCOR1	chr13:48574590-48576716	IMR90	lung:	n/a	n/a
8	POLR2A	chr13:48576169-48576383	Hela-S3	cervix:	n/a	n/a
9	STAT3	chr13:48575919-48576295	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr13:48576054-48576444	Hela-S3	cervix:	n/a	n/a
11	MYC	chr13:48575405-48576343	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr13:48576051-48576263	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr13:48575969-48576258	MCF10A-Er-Src	breast:	n/a	n/a
14	MAX	chr13:48575134-48576429	Hela-S3	cervix:	n/a	n/a
15	MAX	chr13:48575334-48576413	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr13:48574745-48576639	H1-hESC	embryonic stem cell:	n/a	n/a
17	FOS	chr13:48575855-48576253	MCF10A-Er-Src	breast:	n/a	n/a
18	SIN3A	chr13:48576212-48576260	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48573666..48577274-chr13:48610467..48613685,4	MCF-7	breast:
2	chr13:48573863..48576384-chr13:48611584..48613293,2	K562	blood:

Variant related genes	Relation type
SUCLA2	TF binding region
ENSG00000136159	Chromatin interaction
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1098354	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11148099	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11148100	0.80[ASN][1000 genomes]
rs11618397	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1326135	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1326136	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1326138	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1326139	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1326140	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1536301	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17071168	0.84[ASN][1000 genomes]
rs1853929	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1886976	0.84[EUR][1000 genomes]
rs1926089	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2031590	0.82[ASN][1000 genomes]
rs2148243	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2148245	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2182376	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2296574	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2406697	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2406698	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2406699	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4447314	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4522322	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4941621	0.82[ASN][1000 genomes]
rs4942725	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4942727	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4942728	0.80[ASN][1000 genomes]
rs4942729	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4942735	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561417	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6561419	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6561420	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6561424	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561427	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561430	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561431	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6561432	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs718010	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7318770	0.82[ASN][1000 genomes]
rs7319245	0.82[ASN][1000 genomes]
rs7320366	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7320461	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7320759	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7322515	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7324541	0.81[AMR][1000 genomes]
rs7325189	0.80[ASN][1000 genomes]
rs7325437	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7326984	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7327260	0.82[AFR][1000 genomes]
rs7327730	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7328525	0.82[ASN][1000 genomes]
rs7328537	0.82[ASN][1000 genomes]
rs7328549	0.82[AFR][1000 genomes]
rs7329419	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7330130	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7330913	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7331285	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7332304	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7333659	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7333821	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7334207	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7335788	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7337004	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7337744	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7338125	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7338373	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7338894	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs765809	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7990244	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7990266	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7990505	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7997802	0.82[ASN][1000 genomes]
rs7998116	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7998260	0.82[ASN][1000 genomes]
rs7998497	0.82[ASN][1000 genomes]
rs7998998	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8000164	0.82[ASN][1000 genomes]
rs8001432	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9316339	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9316343	0.82[ASN][1000 genomes]
rs9316344	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526417	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526423	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526424	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9526426	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526429	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526430	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526433	0.82[ASN][1000 genomes]
rs9526434	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534877	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534878	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534879	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534880	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534882	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9534885	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534889	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534892	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9534896	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9534897	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9534898	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534901	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534903	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9534904	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534905	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534906	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534907	0.82[ASN][1000 genomes]
rs9534908	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534909	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9534912	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534913	0.82[ASN][1000 genomes]
rs9534922	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534923	0.80[ASN][1000 genomes]
rs9534926	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534929	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9562787	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9567959	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9567960	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9567963	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9567972	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9567976	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9595825	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7999505	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs7999505	SUCLA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48573000-48576600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr13:48573800-48576400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr13:48574200-48576400	Active TSS	Brain Germinal Matrix	brain
4	chr13:48574600-48576400	Active TSS	Hela-S3	cervix
5	chr13:48574600-48576600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr13:48574600-48576600	Active TSS	Brain Cingulate Gyrus	brain
7	chr13:48574800-48576400	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr13:48574800-48576400	Active TSS	Brain Angular Gyrus	brain
9	chr13:48574800-48576400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr13:48574800-48576600	Active TSS	Brain Anterior Caudate	brain
11	chr13:48574800-48576600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr13:48575000-48576600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:48575600-48576400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr13:48575800-48576400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr13:48576000-48576400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:48576000-48576400	Flanking Active TSS	Fetal Muscle Trunk	muscle
17	chr13:48576000-48576400	Active TSS	HepG2	liver
18	chr13:48576000-48576600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr13:48576000-48576600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:48576000-48576600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr13:48576000-48576600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr13:48576000-48576600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:48576000-48576600	Enhancers	Colonic Mucosa	Colon
24	chr13:48576000-48576600	Enhancers	Placenta	Placenta
25	chr13:48576000-48576600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr13:48576000-48576600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr13:48576000-48576600	Active TSS	Stomach Smooth Muscle	stomach
28	chr13:48576000-48576600	Enhancers	HUVEC	blood vessel
29	chr13:48576000-48576600	Enhancers	NHDF-Ad	bronchial
30	chr13:48576000-48576600	Enhancers	NHLF	lung
31	chr13:48576000-48576800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr13:48576000-48576800	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr13:48576000-48576800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr13:48576000-48576800	Enhancers	Fetal Brain Male	brain
35	chr13:48576000-48576800	Enhancers	HMEC	breast
36	chr13:48576000-48577800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr13:48576000-48578000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr13:48576000-48578200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr13:48576000-48578400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr13:48576000-48580200	Weak transcription	HSMM	muscle
41	chr13:48576000-48582800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr13:48576000-48583200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr13:48576000-48583400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr13:48576000-48583400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr13:48576000-48583600	Weak transcription	HSMMtube	muscle
46	chr13:48576000-48583800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr13:48576000-48587000	Weak transcription	Primary B cells from cord blood	blood
48	chr13:48576000-48587000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr13:48576000-48588400	Weak transcription	Fetal Intestine Large	intestine
50	chr13:48576000-48589800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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