Variant report

Variant	rs66599479
Chromosome Location	chr19:41248855-41248856
allele	A/C
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	POLR2A	chr19:41248846-41248899	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr19:41248740-41248890	WERI-Rb-1	eye:	n/a	chr19:41248745-41248758 chr19:41248744-41248760 chr19:41248743-41248761
3	POLR2A	chr19:41247302-41248869	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr19:41248240-41248909	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr19:41247463-41249035	Hela-S3	cervix:	n/a	n/a
6	RAD21	chr19:41248481-41248913	H1-hESC	embryonic stem cell:	n/a	chr19:41248714-41248728 chr19:41248741-41248760
7	POLR2A	chr19:41247331-41248953	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr19:41245709-41249072	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:41247319-41249007	K562	blood:	n/a	n/a
10	POLR2A	chr19:41247390-41248954	K562	blood:	n/a	n/a
11	POLR2A	chr19:41247510-41248894	A549	lung:	n/a	n/a
12	POLR2A	chr19:41247405-41249010	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41222890..41224913-chr19:41248409..41251329,2	MCF-7	breast:
2	chr19:41241471..41243088-chr19:41248764..41251353,2	MCF-7	breast:
3	chr19:41220577..41223187-chr19:41248181..41249684,2	MCF-7	breast:
4	chr19:41246355..41251647-chr19:41252986..41257062,8	MCF-7	breast:
5	chr19:41248854..41252993-chr19:41253162..41257094,7	MCF-7	breast:

Variant related genes	Relation type
C19orf54	TF binding region
ENSG00000077312	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11668501	1.00[ASN][1000 genomes]
rs12983335	1.00[ASN][1000 genomes]
rs12984298	1.00[ASN][1000 genomes]
rs4420642	1.00[ASN][1000 genomes]
rs55993576	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66743282	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66865752	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249805	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253502	1.00[ASN][1000 genomes]
rs7253804	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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41227000-41254600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr19:41227200-41255200	Weak transcription	Fetal Heart	heart
3	chr19:41228600-41250000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:41228600-41251000	Strong transcription	Fetal Brain Female	brain
5	chr19:41229400-41249000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:41229800-41249200	Strong transcription	Thymus	Thymus
7	chr19:41229800-41250400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr19:41233600-41249200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr19:41237000-41255400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:41237600-41255200	Weak transcription	Fetal Brain Male	brain
11	chr19:41239400-41250000	Strong transcription	Spleen	Spleen
12	chr19:41240200-41255600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr19:41241600-41251000	Weak transcription	NH-A	brain
14	chr19:41242000-41250600	Strong transcription	Fetal Intestine Small	intestine
15	chr19:41242000-41253800	Weak transcription	GM12878-XiMat	blood
16	chr19:41242200-41255600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr19:41242400-41251000	Weak transcription	Hela-S3	cervix
18	chr19:41242600-41250200	Strong transcription	Fetal Intestine Large	intestine
19	chr19:41243200-41251200	Weak transcription	Fetal Kidney	kidney
20	chr19:41243400-41254400	Weak transcription	Psoas Muscle	Psoas
21	chr19:41243600-41255600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr19:41243800-41249400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:41243800-41255400	Weak transcription	HSMM	muscle
24	chr19:41244000-41250800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:41245000-41250200	Genic enhancers	Placenta	Placenta
26	chr19:41245000-41251000	Weak transcription	HUVEC	blood vessel
27	chr19:41245000-41254600	Weak transcription	Stomach Mucosa	stomach
28	chr19:41245000-41255400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:41245200-41254400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:41245600-41251000	Weak transcription	Osteobl	bone
31	chr19:41245600-41251200	Weak transcription	HSMMtube	muscle
32	chr19:41245600-41255600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr19:41245800-41249600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:41245800-41249800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:41245800-41255400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr19:41246000-41250000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:41246000-41255600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:41246200-41251000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:41246200-41254400	Weak transcription	Brain Substantia Nigra	brain
40	chr19:41246200-41255400	Weak transcription	Brain Angular Gyrus	brain
41	chr19:41246200-41255400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr19:41246200-41255400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:41246200-41255600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:41246200-41255600	Weak transcription	Small Intestine	intestine
45	chr19:41246200-41256000	Weak transcription	Aorta	Aorta
46	chr19:41246400-41249000	Weak transcription	Brain Germinal Matrix	brain
47	chr19:41246400-41249600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr19:41246400-41250600	Weak transcription	A549	lung
49	chr19:41246400-41254600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr19:41246400-41255000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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