Variant report

Variant	rs55673424
Chromosome Location	chr19:40450700-40450701
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	TCF12	chr19:40449435-40451491	A549	lung:	n/a	chr19:40450846-40450854
2	SP1	chr19:40449499-40451004	A549	lung:	n/a	n/a
3	POLR2A	chr19:40449553-40451259	K562	blood:	n/a	n/a
4	SP1	chr19:40449418-40450951	A549	lung:	n/a	n/a
5	MAX	chr19:40449549-40451091	A549	lung:	n/a	n/a
6	GATA3	chr19:40449611-40450803	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40449986..40451522-chr19:40453683..40455500,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187534	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11878670	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11879271	0.82[ASN][1000 genomes]
rs11880843	1.00[ASN][1000 genomes]
rs11881551	0.86[ASN][1000 genomes]
rs11883342	0.86[ASN][1000 genomes]
rs12052060	0.82[ASN][1000 genomes]
rs55718963	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55838062	0.86[ASN][1000 genomes]
rs55873814	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56040936	0.82[ASN][1000 genomes]
rs56108413	0.82[ASN][1000 genomes]
rs7250934	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73040535	1.00[ASN][1000 genomes]
rs73040537	1.00[ASN][1000 genomes]
rs73040556	0.86[ASN][1000 genomes]
rs73040573	0.86[ASN][1000 genomes]
rs73052630	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv510766	chr19:40344356-40453018	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40446800-40451600	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr19:40446800-40453000	Enhancers	Fetal Intestine Large	intestine
3	chr19:40446800-40453000	Enhancers	Stomach Mucosa	stomach
4	chr19:40447000-40450800	Enhancers	Fetal Thymus	thymus
5	chr19:40447200-40453000	Enhancers	Fetal Intestine Small	intestine
6	chr19:40447400-40451200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr19:40447600-40451000	Weak transcription	Brain Hippocampus Middle	brain
8	chr19:40447600-40451400	Enhancers	Fetal Kidney	kidney
9	chr19:40447800-40451600	Enhancers	Colonic Mucosa	Colon
10	chr19:40447800-40452800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:40447800-40457000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:40448200-40453200	Enhancers	Primary B cells from peripheral blood	blood
13	chr19:40448400-40455600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:40448400-40457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:40448600-40452400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:40448600-40453000	Enhancers	Primary B cells from cord blood	blood
17	chr19:40449000-40450800	Enhancers	Pancreas	Pancrea
18	chr19:40449000-40451200	Enhancers	Adipose Nuclei	Adipose
19	chr19:40449000-40451400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:40449000-40452800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:40449200-40457200	Weak transcription	Small Intestine	intestine
22	chr19:40449600-40451200	Enhancers	Fetal Lung	lung
23	chr19:40449600-40451400	Flanking Active TSS	A549	lung
24	chr19:40449800-40452400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr19:40450000-40451400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr19:40450000-40451600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr19:40450000-40461200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr19:40450000-40461800	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr19:40450200-40451200	Enhancers	Primary T cells from cord blood	blood
30	chr19:40450200-40456600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr19:40450400-40452200	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr19:40450400-40454200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr19:40450400-40458600	Weak transcription	Thymus	Thymus
34	chr19:40450600-40450800	Weak transcription	Lung	lung
35	chr19:40450600-40450800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
36	chr19:40450600-40451200	Weak transcription	Brain Substantia Nigra	brain
37	chr19:40450600-40451400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:40450600-40451600	Enhancers	Duodenum Mucosa	Duodenum
39	chr19:40450600-40451600	Enhancers	Dnd41	blood
40	chr19:40450600-40452400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr19:40450600-40453000	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr19:40450600-40453000	Enhancers	HepG2	liver
43	chr19:40450600-40457200	Enhancers	Primary T helper naive cells from peripheral blood	blood

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