Variant report

Variant	rs59953916
Chromosome Location	chr19:19283722-19283723
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	EGR1	chr19:19283508-19283724	GM12878	blood:	n/a	chr19:19283644-19283658
2	RCOR1	chr19:19282542-19283811	K562	blood:	n/a	n/a
3	JUND	chr19:19283469-19283796	K562	blood:	n/a	n/a
4	TBP	chr19:19283621-19283807	K562	blood:	n/a	n/a
5	RUNX3	chr19:19282844-19283853	GM12878	blood:	n/a	n/a
6	HDAC2	chr19:19283582-19283778	K562	blood:	n/a	n/a
7	ZBTB7A	chr19:19283538-19283745	K562	blood:	n/a	n/a
8	MAZ	chr19:19282709-19283730	K562	blood:	n/a	chr19:19283045-19283054
9	RUNX3	chr19:19283442-19283762	GM12878	blood:	n/a	n/a
10	EGR1	chr19:19283358-19283780	K562	blood:	n/a	chr19:19283644-19283658 chr19:19283504-19283514 chr19:19283504-19283517
11	EGR1	chr19:19283351-19283808	K562	blood:	n/a	chr19:19283644-19283658 chr19:19283504-19283514 chr19:19283504-19283517

No.	Distal block	Cell Line	Cell type
1	chr19:19248991..19251114-chr19:19283513..19286048,2	K562	blood:
2	chr19:19173662..19176225-chr19:19282818..19284543,2	K562	blood:
3	chr19:19171096..19173278-chr19:19281615..19284130,2	K562	blood:
4	chr19:19280728..19282635-chr19:19282932..19284742,2	K562	blood:
5	chr19:19256287..19258012-chr19:19281605..19284547,2	MCF-7	breast:
6	chr19:19276770..19279555-chr19:19281152..19284239,3	K562	blood:

Variant related genes	Relation type
MEF2B	TF binding region
ENSG00000181035	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064545	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10854010	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10854011	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11085254	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1124855	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11668300	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668319	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11671619	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11672862	0.84[EUR][1000 genomes]
rs11878301	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11879715	0.84[EUR][1000 genomes]
rs12162246	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12162274	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12974661	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006991	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2157850	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2283618	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283619	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283622	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28584534	0.84[EUR][1000 genomes]
rs34719098	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35743105	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3819578	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3890384	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4471820	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57157462	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58190593	0.84[EUR][1000 genomes]
rs59829545	0.85[EUR][1000 genomes]
rs60450968	0.84[EUR][1000 genomes]
rs60636572	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61061000	0.81[EUR][1000 genomes]
rs66764858	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66907536	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67238925	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67239864	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67801643	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67845377	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67868334	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72997105	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73535580	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73537429	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73537449	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7360000	0.84[EUR][1000 genomes];0.80[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	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59953916	MEF2B	cis	Thyroid	GTEx
rs59953916	MEF2B	cis	Whole Blood	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19259000-19290200	Weak transcription	Colon Smooth Muscle	Colon
2	chr19:19268800-19287200	Weak transcription	Dnd41	blood
3	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
4	chr19:19280800-19287000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:19280800-19301600	Weak transcription	NHEK	skin
6	chr19:19281000-19287000	Weak transcription	Primary T cells from cord blood	blood
7	chr19:19281200-19283800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:19281200-19283800	Enhancers	GM12878-XiMat	blood
9	chr19:19281200-19287400	Weak transcription	Aorta	Aorta
10	chr19:19281400-19285600	Weak transcription	Right Ventricle	heart
11	chr19:19281400-19286600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:19281400-19287000	Weak transcription	Gastric	stomach
13	chr19:19281400-19287000	Weak transcription	Lung	lung
14	chr19:19281400-19287000	Weak transcription	Thymus	Thymus
15	chr19:19281400-19287400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr19:19281400-19287400	Weak transcription	Esophagus	oesophagus
17	chr19:19281400-19287400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr19:19281400-19290200	Weak transcription	Brain Substantia Nigra	brain
19	chr19:19281400-19292200	Weak transcription	HMEC	breast
20	chr19:19281400-19300800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr19:19281600-19285800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:19281600-19286400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:19281600-19286600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:19281600-19287200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:19281600-19287200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr19:19281600-19287200	Weak transcription	Fetal Intestine Large	intestine
27	chr19:19281600-19287400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:19281600-19289000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr19:19281600-19290400	Weak transcription	Fetal Lung	lung
30	chr19:19281600-19290600	Weak transcription	Fetal Brain Female	brain
31	chr19:19281600-19290800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr19:19281600-19290800	Weak transcription	Brain Angular Gyrus	brain
33	chr19:19281600-19292000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:19281600-19293000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:19281600-19297200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr19:19281600-19299400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:19281600-19300600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:19281600-19302000	Weak transcription	NH-A	brain
39	chr19:19281600-19302200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:19281800-19285800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr19:19281800-19285800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:19281800-19286400	Weak transcription	Fetal Intestine Small	intestine
43	chr19:19281800-19286600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:19281800-19286600	Weak transcription	Fetal Thymus	thymus
45	chr19:19281800-19286600	Weak transcription	Ovary	ovary
46	chr19:19281800-19286800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:19281800-19287000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:19281800-19287000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr19:19281800-19287000	Weak transcription	Pancreas	Pancrea
50	chr19:19281800-19287400	Weak transcription	Brain Anterior Caudate	brain

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