Variant report

Variant	rs55740667
Chromosome Location	chr19:41112605-41112606
allele	C/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	MAX	chr19:41109057-41112684	A549	lung:	n/a	chr19:41109621-41109631 chr19:41110033-41110043 chr19:41112230-41112240 chr19:41109693-41109703 chr19:41110085-41110095
2	MAX	chr19:41112031-41112618	MCF-7	breast:	n/a	chr19:41112230-41112240
3	TCF12	chr19:41107775-41112752	A549	lung:	n/a	chr19:41110897-41110905 chr19:41109793-41109800 chr19:41111228-41111238 chr19:41109824-41109831
4	HDAC2	chr19:41112066-41112638	MCF-7	breast:	n/a	n/a
5	PBX3	chr19:41109279-41112713	A549	lung:	n/a	n/a
6	NR2F2	chr19:41111963-41112675	MCF-7	breast:	n/a	n/a
7	MXI1	chr19:41108742-41112633	SK-N-SH	brain:	n/a	chr19:41112101-41112110
8	MAX	chr19:41106852-41112636	HCT-116	colon:	n/a	chr19:41108140-41108149 chr19:41106996-41107006 chr19:41109621-41109631 chr19:41107680-41107690 chr19:41110033-41110043 chr19:41112230-41112240 chr19:41108141-41108148 chr19:41109693-41109703 chr19:41110085-41110095 chr19:41107176-41107186 chr19:41108976-41108985
9	SIN3AK20	chr19:41110729-41112668	MCF-7	breast:	n/a	n/a
10	POLR2A	chr19:41107198-41112648	SK-N-MC	brain:	n/a	n/a
11	MAX	chr19:41110537-41112613	ECC-1	luminal epithelium:	n/a	chr19:41112230-41112240
12	BCL3	chr19:41107600-41112675	A549	lung:	n/a	chr19:41109906-41109915 chr19:41109623-41109636 chr19:41109787-41109796 chr19:41110189-41110198 chr19:41109814-41109827 chr19:41108090-41108099 chr19:41108193-41108202 chr19:41109619-41109632
13	SMARCB1	chr19:41109412-41112675	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr19:41106762-41114701	K562	blood:	n/a	n/a
15	POLR2A	chr19:41109033-41112641	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr19:41107105-41114419	Hela-S3	cervix:	n/a	n/a
17	MYC	chr19:41110584-41112676	A549	lung:	n/a	chr19:41112230-41112240
18	NFIC	chr19:41111074-41112608	ECC-1	luminal epithelium:	n/a	n/a
19	E2F6	chr19:41110693-41112688	A549	lung:	n/a	chr19:41111202-41111209 chr19:41111202-41111209 chr19:41111201-41111213 chr19:41111604-41111613 chr19:41111198-41111212 chr19:41111201-41111210 chr19:41111202-41111209
20	POLR2A	chr19:41109440-41112619	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr19:41111933-41112651	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40949716..40951577-chr19:41110913..41113250,2	MCF-7	breast:
2	chr19:41107019..41113650-chr19:41128672..41134191,9	K562	blood:
3	chr19:41110008..41112738-chr19:41221401..41222982,2	MCF-7	breast:
4	chr19:41031800..41041078-chr19:41106134..41114466,15	K562	blood:
5	chr19:41029343..41031510-chr19:41110822..41112773,2	K562	blood:
6	chr19:41108422..41113817-chr19:41128876..41134100,7	MCF-7	breast:
7	chr19:41085326..41087014-chr19:41111763..41113290,2	K562	blood:
8	chr19:41112293..41113971-chr4:140476001..140478428,2	MCF-7	breast:
9	chr19:41106677..41108260-chr19:41111446..41113264,2	MCF-7	breast:
10	chr19:40970298..40972674-chr19:41110467..41112716,3	MCF-7	breast:

Variant related genes	Relation type
LTBP4	TF binding region
ENSG00000160460	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000272717	Chromatin interaction
ENSG00000090013	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000145391	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11083560	0.88[ASN][1000 genomes]
rs2246761	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278243	0.81[EUR][1000 genomes]
rs2303728	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786527	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41512448	0.81[EUR][1000 genomes]
rs4802079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55815263	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62107907	0.91[ASN][1000 genomes]
rs62107911	0.90[ASN][1000 genomes]
rs62107913	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73047963	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73047967	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
13	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
14	nsv911725	chr19:41090190-41114065	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
16	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
17	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41106000-41136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41109600-41113600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:41109800-41122600	Weak transcription	Aorta	Aorta
4	chr19:41110000-41118200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:41111000-41112800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr19:41111600-41113000	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr19:41112000-41112800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:41112000-41114200	Bivalent Enhancer	Fetal Stomach	stomach
9	chr19:41112000-41114800	Weak transcription	Fetal Kidney	kidney
10	chr19:41112000-41115200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr19:41112000-41115200	Weak transcription	HUVEC	blood vessel
12	chr19:41112000-41115600	Weak transcription	Brain Angular Gyrus	brain
13	chr19:41112000-41115600	Weak transcription	Brain Anterior Caudate	brain
14	chr19:41112000-41116000	Enhancers	Stomach Mucosa	stomach
15	chr19:41112000-41116200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:41112000-41116200	Weak transcription	NHLF	lung
17	chr19:41112200-41112800	Bivalent Enhancer	Primary B cells from cord blood	blood
18	chr19:41112200-41112800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:41112200-41112800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:41112200-41112800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:41112200-41113200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:41112200-41113200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:41112200-41113400	Weak transcription	Adipose Nuclei	Adipose
24	chr19:41112200-41113400	Weak transcription	Left Ventricle	heart
25	chr19:41112200-41113400	Weak transcription	Lung	lung
26	chr19:41112200-41113400	Weak transcription	Ovary	ovary
27	chr19:41112200-41113400	Weak transcription	Right Atrium	heart
28	chr19:41112200-41114000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr19:41112200-41114400	Enhancers	Esophagus	oesophagus
30	chr19:41112200-41115200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:41112200-41115200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:41112200-41115200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr19:41112200-41115200	Weak transcription	Fetal Lung	lung
34	chr19:41112200-41115200	Weak transcription	Osteobl	bone
35	chr19:41112200-41115400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:41112200-41115400	Weak transcription	Gastric	stomach
37	chr19:41112200-41115400	Weak transcription	Psoas Muscle	Psoas
38	chr19:41112200-41115400	Weak transcription	Small Intestine	intestine
39	chr19:41112200-41115400	Weak transcription	HSMM	muscle
40	chr19:41112400-41112800	Active TSS	Primary T cells from cord blood	blood
41	chr19:41112400-41113200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr19:41112400-41113200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:41112400-41113200	Weak transcription	Pancreas	Pancrea
44	chr19:41112400-41113200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:41112400-41113400	Weak transcription	Right Ventricle	heart
46	chr19:41112400-41113400	Weak transcription	NHEK	skin
47	chr19:41112400-41113600	Enhancers	Primary B cells from peripheral blood	blood
48	chr19:41112400-41114000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:41112400-41114000	Bivalent Enhancer	HepG2	liver
50	chr19:41112400-41114400	Flanking Active TSS	Hela-S3	cervix

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