Variant report

Variant	rs6820684
Chromosome Location	chr4:190863742-190863743
allele	A/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	RCOR1	chr4:190863514-190863773	GM12878	blood:	n/a	n/a
2	EBF1	chr4:190863364-190863921	GM12878	blood:	n/a	n/a
3	ZBTB33	chr4:190863382-190864055	HepG2	liver:	n/a	n/a
4	RCOR1	chr4:190863347-190863833	K562	blood:	n/a	n/a
5	EBF1	chr4:190863519-190864055	GM12878	blood:	n/a	n/a
6	MXI1	chr4:190861204-190863821	IMR90	lung:	n/a	n/a
7	CTCF	chr4:190863600-190863750	HPAF	blood vessel:	n/a	n/a
8	GATA2	chr4:190863309-190863943	K562	blood:	n/a	n/a
9	HEY1	chr4:190863371-190863938	K562	blood:	n/a	n/a
10	EP300	chr4:190862782-190863746	K562	blood:	n/a	chr4:190863079-190863092
11	STAT5A	chr4:190863288-190863978	K562	blood:	n/a	n/a
12	BATF	chr4:190863522-190863941	GM12878	blood:	n/a	n/a
13	EBF1	chr4:190863707-190864052	GM12878	blood:	n/a	n/a
14	SP1	chr4:190863349-190864252	HepG2	liver:	n/a	n/a
15	POU2F2	chr4:190863357-190864012	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000245685	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10001956	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11132770	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11132771	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11736387	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12641802	0.90[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap]
rs12646565	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12646667	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12646672	0.80[EUR][1000 genomes]
rs12649488	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12649515	0.80[EUR][1000 genomes]
rs13121836	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13121986	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13133725	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13133958	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13141640	0.80[AMR][1000 genomes]
rs13148101	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1961818	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2037947	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2037948	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2078634	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2411549	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4145515	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4145516	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4145517	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6553396	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816856	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6837422	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7657916	0.87[EUR][1000 genomes]
rs7658339	0.87[EUR][1000 genomes]
rs7668489	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7691161	0.83[EUR][1000 genomes]
rs9992042	0.83[EUR][1000 genomes]
rs9996679	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6820684	FRG1	cis	multi-tissue	Pritchard
rs6820684	AF146191.4	cis	Esophagus Muscularis	GTEx
rs6820684	AF146191.4	cis	Thyroid	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:190858600-190865400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr4:190860600-190864200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
3	chr4:190860800-190863800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
4	chr4:190860800-190863800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
5	chr4:190860800-190863800	ZNF genes & repeats	Fetal Brain Male	brain
6	chr4:190860800-190864000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
7	chr4:190861000-190863800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:190861000-190863800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr4:190861200-190863800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:190861200-190863800	ZNF genes & repeats	HMEC	breast
11	chr4:190861600-190863800	Active TSS	Psoas Muscle	Psoas
12	chr4:190861600-190863800	Active TSS	Right Ventricle	heart
13	chr4:190861600-190864200	Active TSS	Aorta	Aorta
14	chr4:190861600-190864200	Active TSS	GM12878-XiMat	blood
15	chr4:190861800-190863800	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr4:190862600-190863800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:190862600-190868800	Weak transcription	Lung	lung
18	chr4:190862600-190868800	Weak transcription	Pancreas	Pancrea
19	chr4:190862600-190869800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:190862600-190881000	Weak transcription	Spleen	Spleen
21	chr4:190862800-190863800	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr4:190862800-190863800	Enhancers	Small Intestine	intestine
23	chr4:190862800-190864200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr4:190862800-190865200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:190862800-190867000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:190863000-190863800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr4:190863000-190863800	Enhancers	Primary B cells from peripheral blood	blood
28	chr4:190863000-190864200	Enhancers	Brain Cingulate Gyrus	brain
29	chr4:190863000-190864400	Flanking Active TSS	Dnd41	blood
30	chr4:190863000-190864800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:190863000-190866600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:190863000-190880800	Weak transcription	Brain Angular Gyrus	brain
33	chr4:190863200-190863800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:190863200-190863800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:190863200-190863800	Enhancers	Fetal Stomach	stomach
36	chr4:190863200-190863800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr4:190863200-190864000	Enhancers	Primary B cells from cord blood	blood
38	chr4:190863200-190864000	Enhancers	Adipose Nuclei	Adipose
39	chr4:190863200-190864200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr4:190863200-190864200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:190863200-190864200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr4:190863200-190864200	Enhancers	Liver	Liver
43	chr4:190863200-190864200	Enhancers	Ovary	ovary
44	chr4:190863200-190864400	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr4:190863200-190864600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr4:190863200-190864600	Enhancers	Colon Smooth Muscle	Colon
47	chr4:190863200-190864800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr4:190863200-190865000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:190863200-190866000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:190863200-190866400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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