Variant report

Variant	rs2238668
Chromosome Location	chr19:19282597-19282598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19282594-19283265	HL-60	blood:	n/a	n/a
2	POLR2A	chr19:19282363-19283579	K562	blood:	n/a	n/a
3	RCOR1	chr19:19282542-19283811	K562	blood:	n/a	n/a
4	CBX3	chr19:19282595-19282894	K562	blood:	n/a	n/a
5	FOXA2	chr19:19282527-19283243	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:19282593-19282599	MCF-7	breast:	n/a	n/a
7	POLR2A	chr19:19282529-19282764	GM12878	blood:	n/a	n/a
8	CBX3	chr19:19282587-19283440	K562	blood:	n/a	n/a
9	JUN	chr19:19282160-19283412	K562	blood:	n/a	n/a
10	MAZ	chr19:19282597-19283374	IMR90	lung:	n/a	chr19:19283045-19283054
11	MTA3	chr19:19282529-19283404	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:19282281-19283398	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:19282567-19283257	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr19:19282549-19283288	GM12878	blood:	n/a	n/a
15	TEAD4	chr19:19282595-19283129	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19254048..19257177-chr19:19281420..19283386,3	K562	blood:
2	chr19:19171096..19173278-chr19:19281615..19284130,2	K562	blood:
3	chr19:19281578..19283666-chr19:19326802..19329714,2	K562	blood:
4	chr19:19280114..19282646-chr19:19429552..19431405,2	MCF-7	breast:
5	chr19:19256287..19258012-chr19:19281605..19284547,2	MCF-7	breast:
6	chr19:19279506..19282646-chr19:19302669..19304636,3	MCF-7	breast:
7	chr19:19276770..19279555-chr19:19281152..19284239,3	K562	blood:
8	chr19:19281703..19283642-chr19:19290423..19292438,2	MCF-7	breast:

No data

Variant related genes	Relation type
MEF2B	TF binding region
ENSG00000254901	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000213999	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1005980	0.91[ASN][1000 genomes]
rs10417796	0.84[EUR][1000 genomes]
rs10418053	0.84[EUR][1000 genomes]
rs1050544	0.85[EUR][1000 genomes]
rs10854008	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10854009	0.83[EUR][1000 genomes]
rs10854012	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11669408	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11669860	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11669861	0.88[EUR][1000 genomes]
rs12609573	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12972894	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12974672	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12975096	0.81[EUR][1000 genomes]
rs12975253	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12975290	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12980269	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12980955	0.85[EUR][1000 genomes]
rs12981160	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858846	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2239370	0.83[EUR][1000 genomes]
rs2283623	0.85[EUR][1000 genomes]
rs2314035	0.84[EUR][1000 genomes]
rs35342977	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3787040	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808185	0.82[EUR][1000 genomes]
rs539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62135499	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71332145	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7256811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7260127	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72997174	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs741706	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs759999	0.80[EUR][1000 genomes]
rs8101388	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19249600-19282600	Weak transcription	NHLF	lung
2	chr19:19259000-19290200	Weak transcription	Colon Smooth Muscle	Colon
3	chr19:19268200-19282600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:19268800-19287200	Weak transcription	Dnd41	blood
5	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
6	chr19:19280800-19287000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:19280800-19301600	Weak transcription	NHEK	skin
8	chr19:19281000-19283400	Enhancers	Placenta	Placenta
9	chr19:19281000-19287000	Weak transcription	Primary T cells from cord blood	blood
10	chr19:19281200-19282600	Weak transcription	Psoas Muscle	Psoas
11	chr19:19281200-19282800	Weak transcription	Liver	Liver
12	chr19:19281200-19282800	Weak transcription	HSMM	muscle
13	chr19:19281200-19283000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:19281200-19283800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:19281200-19283800	Enhancers	GM12878-XiMat	blood
16	chr19:19281200-19287400	Weak transcription	Aorta	Aorta
17	chr19:19281400-19282600	Weak transcription	HSMMtube	muscle
18	chr19:19281400-19282800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:19281400-19282800	Enhancers	K562	blood
20	chr19:19281400-19283000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr19:19281400-19283000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:19281400-19283400	Enhancers	Adipose Nuclei	Adipose
23	chr19:19281400-19285600	Weak transcription	Right Ventricle	heart
24	chr19:19281400-19286600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:19281400-19287000	Weak transcription	Gastric	stomach
26	chr19:19281400-19287000	Weak transcription	Lung	lung
27	chr19:19281400-19287000	Weak transcription	Thymus	Thymus
28	chr19:19281400-19287400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr19:19281400-19287400	Weak transcription	Esophagus	oesophagus
30	chr19:19281400-19287400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr19:19281400-19290200	Weak transcription	Brain Substantia Nigra	brain
32	chr19:19281400-19292200	Weak transcription	HMEC	breast
33	chr19:19281400-19300800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr19:19281600-19282600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:19281600-19282600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr19:19281600-19282600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr19:19281600-19285800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr19:19281600-19286400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr19:19281600-19286600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:19281600-19287200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr19:19281600-19287200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:19281600-19287200	Weak transcription	Fetal Intestine Large	intestine
43	chr19:19281600-19287400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:19281600-19289000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr19:19281600-19290400	Weak transcription	Fetal Lung	lung
46	chr19:19281600-19290600	Weak transcription	Fetal Brain Female	brain
47	chr19:19281600-19290800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr19:19281600-19290800	Weak transcription	Brain Angular Gyrus	brain
49	chr19:19281600-19292000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:19281600-19293000	Weak transcription	H9 Cell Line	embryonic stem cell

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