Variant report

Variant	rs3787045
Chromosome Location	chr19:18959448-18959449
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	CTCF	chr19:18959340-18959490	GM12865	blood:	n/a	n/a
2	TCF12	chr19:18958502-18959460	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr19:18958519-18959545	SH-SY5Y	brain:	n/a	chr19:18959103-18959111
4	GATA2	chr19:18958856-18960797	SH-SY5Y	brain:	n/a	chr19:18960399-18960406 chr19:18959103-18959111 chr19:18960392-18960408 chr19:18960394-18960406
5	SPI1	chr19:18959423-18959973	GM12878	blood:	n/a	chr19:18959675-18959688 chr19:18959676-18959685
6	POLR2A	chr19:18959434-18960077	HUVEC	blood vessel:	n/a	n/a
7	CTCF	chr19:18957785-18959604	SK-N-SH	brain:	n/a	chr19:18958185-18958201 chr19:18958293-18958306 chr19:18958186-18958199 chr19:18958179-18958200 chr19:18958184-18958202
8	SMC3	chr19:18957693-18960660	SK-N-SH	brain:	n/a	chr19:18958186-18958200
9	RAD21	chr19:18957629-18960789	SK-N-SH	brain:	n/a	chr19:18958182-18958201 chr19:18958184-18958196 chr19:18958145-18958159
10	MXI1	chr19:18957665-18960817	SK-N-SH	brain:	n/a	chr19:18959924-18959933 chr19:18959926-18959935 chr19:18959926-18959935
11	TCF12	chr19:18957897-18959481	SK-N-SH	brain:	n/a	n/a
12	MXI1	chr19:18959013-18960461	IMR90	lung:	n/a	chr19:18959924-18959933 chr19:18959926-18959935 chr19:18959926-18959935
13	FOS	chr19:18959315-18960271	HUVEC	blood vessel:	n/a	chr19:18959397-18959406

No.	Distal block	Cell Line	Cell type
1	chr19:18698544..18700812-chr19:18957924..18960532,2	MCF-7	breast:
2	chr19:18959107..18961102-chr19:18969761..18972527,2	MCF-7	breast:
3	chr19:18958350..18961503-chr19:18963621..18967114,6	K562	blood:
4	chr19:18958703..18961204-chr19:19005451..19007447,2	MCF-7	breast:

Variant related genes	Relation type
UPF1	TF binding region
ENSG00000006015	Chromatin interaction
ENSG00000130283	Chromatin interaction
ENSG00000223802	Chromatin interaction
ENSG00000005007	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10405364	1.00[ASN][1000 genomes]
rs10420445	1.00[ASN][1000 genomes]
rs11665939	0.94[ASN][1000 genomes]
rs11667922	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669119	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670447	0.96[ASN][1000 genomes]
rs11670952	1.00[ASN][1000 genomes]
rs57030846	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73923167	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73923168	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73923171	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73923173	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73923178	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers 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	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv911299	chr19:18939954-18984843	Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18951000-18960800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:18951800-18977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:18952000-18961200	Weak transcription	Small Intestine	intestine
4	chr19:18953200-18977600	Weak transcription	Fetal Heart	heart
5	chr19:18954200-18961400	Weak transcription	Aorta	Aorta
6	chr19:18954800-18979800	Strong transcription	Dnd41	blood
7	chr19:18955200-18960400	Genic enhancers	GM12878-XiMat	blood
8	chr19:18955400-18963800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:18955600-18961600	Genic enhancers	Pancreas	Pancrea
10	chr19:18955600-18966600	Genic enhancers	Fetal Muscle Leg	muscle
11	chr19:18955800-18961200	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr19:18956200-18978400	Strong transcription	Thymus	Thymus
13	chr19:18956400-18959800	Strong transcription	K562	blood
14	chr19:18956400-18961200	Genic enhancers	Liver	Liver
15	chr19:18956600-18961800	Genic enhancers	Fetal Stomach	stomach
16	chr19:18956600-18962200	Genic enhancers	NHEK	skin
17	chr19:18956600-18972000	Genic enhancers	Fetal Muscle Trunk	muscle
18	chr19:18956800-18960600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr19:18956800-18966800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:18956800-18975200	Strong transcription	HepG2	liver
21	chr19:18957000-18959800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:18957200-18959800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:18957200-18960800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:18957400-18961000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:18957800-18959800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr19:18957800-18960000	Enhancers	Osteobl	bone
27	chr19:18957800-18960600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:18957800-18960800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:18957800-18961000	Enhancers	Left Ventricle	heart
30	chr19:18957800-18961400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:18957800-18961600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:18957800-18961800	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr19:18957800-18962200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr19:18957800-18962200	Enhancers	Ovary	ovary
35	chr19:18958000-18959800	Enhancers	Fetal Brain Male	brain
36	chr19:18958000-18959800	Weak transcription	NH-A	brain
37	chr19:18958000-18961000	Enhancers	Brain Substantia Nigra	brain
38	chr19:18958000-18961200	Genic enhancers	Primary B cells from cord blood	blood
39	chr19:18958200-18960400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:18958200-18960600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr19:18958200-18960800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:18958200-18964600	Genic enhancers	Fetal Thymus	thymus
43	chr19:18958200-18966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:18958200-18977000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:18958400-18959600	Genic enhancers	Brain Inferior Temporal Lobe	brain
46	chr19:18958400-18959600	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr19:18958400-18959600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr19:18958400-18959800	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr19:18958400-18959800	Strong transcription	Fetal Intestine Small	intestine
50	chr19:18958400-18961000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood

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