Variant report

Variant	rs8109544
Chromosome Location	chr19:40946557-40946558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:40945235-40946818	GM12891	blood:	n/a	n/a
2	POLR2A	chr19:40946072-40947001	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:40945070-40946567	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr19:40945036-40947489	K562	blood:	n/a	n/a
5	POLR2A	chr19:40944883-40955137	K562	blood:	n/a	n/a
6	POLR2A	chr19:40946384-40946593	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr19:40945126-40947129	K562	blood:	n/a	n/a
8	POLR2A	chr19:40946321-40946657	HCT-116	colon:	n/a	n/a
9	POLR2A	chr19:40944976-40947714	PFSK-1	brain:	n/a	n/a
10	ZNF384	chr19:40946542-40946992	K562	blood:	n/a	n/a
11	POLR2A	chr19:40945946-40946669	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:40946261-40946731	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:40945123-40946692	HCT-116	colon:	n/a	n/a
14	TEAD4	chr19:40946024-40946635	K562	blood:	n/a	n/a
15	TCF12	chr19:40945861-40946612	A549	lung:	n/a	n/a
16	POLR2A	chr19:40945285-40946990	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr19:40946502-40946737	GM12891	blood:	n/a	n/a
18	POLR2A	chr19:40945945-40946638	GM12891	blood:	n/a	n/a
19	JUND	chr19:40945067-40946719	A549	lung:	n/a	chr19:40946107-40946115
20	POLR2A	chr19:40945774-40946722	K562	blood:	n/a	n/a
21	PML	chr19:40945958-40946766	K562	blood:	n/a	n/a
22	POLR2A	chr19:40945322-40947283	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:40945209-40950245	A549	lung:	n/a	n/a
24	POLR2A	chr19:40945179-40946747	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:40945206-40946956	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr19:40945262-40946666	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr19:40945961-40946672	GM12891	blood:	n/a	n/a
28	MTA3	chr19:40945093-40946657	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:40945108-40946807	PANC-1	pancreas:	n/a	n/a
30	CEBPB	chr19:40946511-40947042	A549	lung:	n/a	n/a
31	POLR2A	chr19:40944978-40947626	SK-N-MC	brain:	n/a	n/a
32	POLR2A	chr19:40946373-40946668	A549	lung:	n/a	n/a
33	POLR2A	chr19:40945886-40946760	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr19:40945901-40947057	K562	blood:	n/a	n/a
35	POLR2A	chr19:40945117-40947505	GM12878	blood:	n/a	n/a
36	TCF12	chr19:40945180-40946852	A549	lung:	n/a	n/a
37	POLR2A	chr19:40946522-40946662	A549	lung:	n/a	n/a
38	BCL3	chr19:40945096-40946636	A549	lung:	n/a	n/a
39	POLR2A	chr19:40945883-40946812	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:40945894-40946738	GM12891	blood:	n/a	n/a
41	POLR2A	chr19:40945208-40946679	K562	blood:	n/a	n/a
42	POLR2A	chr19:40944253-40951075	MCF-7	breast:	n/a	n/a
43	POLR2A	chr19:40946330-40946731	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr19:40945352-40946729	HepG2	liver:	n/a	n/a
45	POLR2A	chr19:40945931-40946704	K562	blood:	n/a	n/a
46	POLR2A	chr19:40945776-40946748	GM12892	blood:	n/a	n/a
47	POLR2A	chr19:40945887-40947498	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40930168..40933020-chr19:40943160..40946840,3	MCF-7	breast:
2	chr19:40851266..40855955-chr19:40945466..40950850,6	K562	blood:
3	chr19:40945209..40947044-chr19:41022798..41025322,2	MCF-7	breast:
4	chr19:40930428..40932998-chr19:40942999..40947020,6	K562	blood:
5	chr19:40945484..40955522-chr19:40966442..40973559,31	MCF-7	breast:
6	chr19:40908387..40911091-chr19:40944867..40946978,2	MCF-7	breast:
7	chr19:40925098..40933993-chr19:40944045..40956524,41	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268366	TF binding region
ENSG00000105223	Chromatin interaction
ENSG00000197019	Chromatin interaction
ENSG00000090013	Chromatin interaction
ENSG00000160460	Chromatin interaction
ENSG00000160392	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56743160	1.00[AMR][1000 genomes]
rs58341807	1.00[AMR][1000 genomes]
rs58675277	1.00[AMR][1000 genomes]
rs7249252	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]

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	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
3	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
4	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
5	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
6	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
7	nsv911709	chr19:40928944-41060616	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 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	chr19:40939800-40946600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:40939800-40948200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr19:40939800-40948200	Weak transcription	Small Intestine	intestine
4	chr19:40940200-40946600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:40940200-40948000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:40940400-40946600	Weak transcription	Brain Hippocampus Middle	brain
7	chr19:40940400-40946600	Weak transcription	Pancreas	Pancrea
8	chr19:40940400-40946600	Weak transcription	Psoas Muscle	Psoas
9	chr19:40940400-40946800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:40940400-40946800	Weak transcription	Primary T cells from cord blood	blood
11	chr19:40940400-40946800	Weak transcription	Brain Anterior Caudate	brain
12	chr19:40940400-40947000	Weak transcription	Aorta	Aorta
13	chr19:40940400-40947000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:40940400-40947000	Weak transcription	Brain Substantia Nigra	brain
15	chr19:40940400-40947000	Weak transcription	Fetal Heart	heart
16	chr19:40940400-40947000	Weak transcription	Dnd41	blood
17	chr19:40940400-40947800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr19:40940400-40948200	Weak transcription	Fetal Brain Male	brain
19	chr19:40940400-40948400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:40940400-40948600	Weak transcription	Brain Angular Gyrus	brain
21	chr19:40940600-40947000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr19:40941200-40946600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:40941400-40946600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr19:40941400-40947000	Weak transcription	Hela-S3	cervix
25	chr19:40941400-40948400	Weak transcription	Stomach Mucosa	stomach
26	chr19:40942600-40946600	Weak transcription	HepG2	liver
27	chr19:40943600-40946600	Strong transcription	Fetal Stomach	stomach
28	chr19:40943600-40948200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr19:40944200-40946800	Strong transcription	Placenta	Placenta
30	chr19:40944200-40947400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:40944800-40947000	Strong transcription	Fetal Intestine Large	intestine
32	chr19:40945000-40946800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr19:40945200-40946600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:40945200-40947800	Genic enhancers	Fetal Muscle Leg	muscle
35	chr19:40945200-40948200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
36	chr19:40945400-40946800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:40945400-40947000	Strong transcription	A549	lung
38	chr19:40945400-40947800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:40945400-40947800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:40945400-40947800	Strong transcription	Brain Germinal Matrix	brain
41	chr19:40945400-40947800	Strong transcription	NHLF	lung
42	chr19:40945400-40948000	Strong transcription	NH-A	brain
43	chr19:40945400-40948400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:40945600-40947400	Strong transcription	Fetal Intestine Small	intestine
45	chr19:40945600-40947600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:40945800-40947000	Strong transcription	Liver	Liver
47	chr19:40945800-40947800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:40945800-40948000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr19:40945800-40948000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
50	chr19:40946000-40946600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links