Variant report

Variant	rs7249252
Chromosome Location	chr19:40899191-40899192
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	chr19:40898725-40899292	MCF-7	breast:	n/a	chr19:40898995-40899013 chr19:40898998-40899011
2	RAD21	chr19:40898618-40899411	HCT-116	colon:	n/a	chr19:40899001-40899011 chr19:40898999-40899012
3	CTCF	chr19:40898058-40899433	A549	lung:	n/a	chr19:40898995-40899013 chr19:40898998-40899011
4	SIN3AK20	chr19:40898545-40899420	MCF-7	breast:	n/a	n/a
5	EP300	chr19:40898586-40899220	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr19:40898685-40899216	ECC-1	luminal epithelium:	n/a	n/a
7	HDAC2	chr19:40898652-40899255	MCF-7	breast:	n/a	n/a
8	RAD21	chr19:40898576-40899312	HCT-116	colon:	n/a	chr19:40899001-40899011 chr19:40898999-40899012
9	TCF12	chr19:40898648-40899283	ECC-1	luminal epithelium:	n/a	chr19:40899005-40899015
10	HDAC2	chr19:40898708-40899237	MCF-7	breast:	n/a	n/a
11	RAD21	chr19:40898779-40899375	MCF-7	breast:	n/a	chr19:40899001-40899011 chr19:40898999-40899012
12	GABPA	chr19:40898593-40899225	MCF-7	breast:	n/a	n/a
13	RAD21	chr19:40898718-40899223	H1-hESC	embryonic stem cell:	n/a	chr19:40899001-40899011 chr19:40898999-40899012
14	RAD21	chr19:40898758-40899314	ECC-1	luminal epithelium:	n/a	chr19:40899001-40899011 chr19:40898999-40899012
15	MAX	chr19:40898706-40899257	MCF-7	breast:	n/a	n/a
16	RAD21	chr19:40898738-40899220	ECC-1	luminal epithelium:	n/a	chr19:40899001-40899011 chr19:40898999-40899012
17	CTCF	chr19:40898643-40899301	HCT-116	colon:	n/a	chr19:40898995-40899013 chr19:40898998-40899011
18	RAD21	chr19:40898730-40899258	MCF-7	breast:	n/a	chr19:40899001-40899011 chr19:40898999-40899012
19	GATA3	chr19:40898639-40899243	MCF-7	breast:	n/a	n/a
20	BCL3	chr19:40898591-40899558	A549	lung:	n/a	n/a
21	ELF1	chr19:40898697-40899191	MCF-7	breast:	n/a	n/a
22	RAD21	chr19:40898759-40899218	A549	lung:	n/a	chr19:40899001-40899011 chr19:40898999-40899012
23	RAD21	chr19:40898731-40899322	A549	lung:	n/a	chr19:40899001-40899011 chr19:40898999-40899012
24	CTCF	chr19:40898747-40899215	A549	lung:	n/a	chr19:40898995-40899013 chr19:40898998-40899011
25	ZBTB7A	chr19:40898670-40899315	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr19:40898712-40899227	ECC-1	luminal epithelium:	n/a	n/a
27	CTCF	chr19:40899120-40899270	A549	lung:	n/a	n/a
28	CTCF	chr19:40899060-40899210	HFF-Myc	foreskin:	n/a	n/a
29	CTCF	chr19:40898723-40899291	MCF-7	breast:	n/a	chr19:40898995-40899013 chr19:40898998-40899011
30	TCF12	chr19:40898629-40899311	ECC-1	luminal epithelium:	n/a	chr19:40899005-40899015

No.	Distal block	Cell Line	Cell type
1	chr19:40892405..40895526-chr19:40897189..40900224,3	MCF-7	breast:
2	chr19:40893982..40897110-chr19:40897355..40900242,3	MCF-7	breast:
3	chr19:40897656..40899719-chr19:40900459..40902541,2	K562	blood:
4	chr19:40898960..40899502-chr19:40931017..40931746,2	MCF-7	breast:
5	chr19:40898268..40902759-chr19:40908036..40910900,5	MCF-7	breast:
6	chr19:40898180..40900295-chr19:40948900..40951381,2	MCF-7	breast:
7	chr19:40898297..40901896-chr19:40902195..40905165,4	MCF-7	breast:
8	chr19:40886017..40887582-chr19:40898990..40901198,2	MCF-7	breast:
9	chr19:40898538..40899440-chr19:40927128..40927843,2	MCF-7	breast:
10	chr19:40897692..40902504-chr19:40929009..40933470,4	MCF-7	breast:

Variant related genes	Relation type
HIPK4	TF binding region
ENSG00000197019	Chromatin interaction
ENSG00000160396	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000167565	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs56743160	1.00[AMR][1000 genomes]
rs58341807	1.00[AMR][1000 genomes]
rs58675277	1.00[AMR][1000 genomes]
rs61208274	1.00[AMR][1000 genomes]
rs7256297	1.00[AMR][1000 genomes]
rs73553624	1.00[AMR][1000 genomes]
rs73553657	1.00[AMR][1000 genomes]
rs73555546	1.00[AMR][1000 genomes]
rs73555594	1.00[AMR][1000 genomes]
rs73557743	1.00[AMR][1000 genomes]
rs73557755	1.00[AMR][1000 genomes]
rs73559610	1.00[AMR][1000 genomes]
rs73559649	1.00[AMR][1000 genomes]
rs8107448	1.00[AMR][1000 genomes]
rs8109544	1.00[AMR][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	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer 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 miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
7	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

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40872800-40904400	Weak transcription	Right Atrium	heart
2	chr19:40885000-40904400	Weak transcription	Fetal Lung	lung
3	chr19:40885000-40909200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:40885000-40909200	Weak transcription	Aorta	Aorta
5	chr19:40885200-40904200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:40885400-40909600	Weak transcription	Pancreas	Pancrea
7	chr19:40886800-40904200	Weak transcription	Right Ventricle	heart
8	chr19:40886800-40909200	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:40887000-40909000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:40887400-40901600	Weak transcription	Fetal Intestine Small	intestine
11	chr19:40887400-40909000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr19:40887600-40900600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:40887800-40901200	Weak transcription	Fetal Stomach	stomach
14	chr19:40887800-40909200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr19:40890000-40904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:40893400-40903000	Weak transcription	Fetal Muscle Leg	muscle
17	chr19:40894800-40909000	Weak transcription	Hela-S3	cervix
18	chr19:40896200-40901800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr19:40897600-40899800	Enhancers	Placenta	Placenta
20	chr19:40897800-40904200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr19:40898000-40899200	Enhancers	Lung	lung
22	chr19:40898000-40899600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:40898000-40899600	Enhancers	Esophagus	oesophagus
24	chr19:40898000-40900200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr19:40898000-40901400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:40898200-40899600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:40898200-40899600	Enhancers	Gastric	stomach
28	chr19:40898200-40899800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr19:40898400-40899600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:40898600-40899200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:40898600-40899400	Enhancers	HMEC	breast
32	chr19:40898600-40899400	Enhancers	NHEK	skin
33	chr19:40898600-40899600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr19:40898600-40899600	Enhancers	Spleen	Spleen
35	chr19:40898600-40899800	Enhancers	A549	lung
36	chr19:40898800-40899200	Enhancers	Fetal Muscle Trunk	muscle
37	chr19:40898800-40899200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr19:40898800-40899200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr19:40898800-40899400	Enhancers	Ovary	ovary
40	chr19:40898800-40899400	Enhancers	Stomach Mucosa	stomach
41	chr19:40898800-40899800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:40899000-40899400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:40899000-40899400	Bivalent Enhancer	HepG2	liver
44	chr19:40899000-40900200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:40899000-40900400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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