Variant report

Variant	rs507512
Chromosome Location	chr19:39922287-39922288
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	POLR2A	chr19:39921090-39922499	HCT-116	colon:	n/a	n/a
2	POLR2A	chr19:39921310-39922489	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr19:39920860-39927633	U87	brain:	n/a	n/a
4	POLR2A	chr19:39921133-39922287	U87	brain:	n/a	n/a
5	MYC	chr19:39920994-39922984	A549	lung:	n/a	chr19:39921744-39921754 chr19:39921458-39921467 chr19:39922371-39922381
6	JUND	chr19:39921086-39922488	A549	lung:	n/a	chr19:39921458-39921466 chr19:39921457-39921466 chr19:39921456-39921467 chr19:39921454-39921465 chr19:39921459-39921466 chr19:39921458-39921467 chr19:39922370-39922379 chr19:39922373-39922382 chr19:39922371-39922380
7	POLR2A	chr19:39921036-39927449	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:39920920-39927829	PFSK-1	brain:	n/a	n/a
9	JUND	chr19:39920490-39925442	A549	lung:	n/a	chr19:39921458-39921466 chr19:39924892-39924906 chr19:39921457-39921466 chr19:39921456-39921467 chr19:39921454-39921465 chr19:39921459-39921466 chr19:39921458-39921467 chr19:39922370-39922379 chr19:39922373-39922382 chr19:39922371-39922380
10	POLR2A	chr19:39920391-39924937	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:39921224-39922324	GM18505	blood:	n/a	n/a
12	POLR2A	chr19:39921189-39922473	GM12878	blood:	n/a	n/a
13	JUND	chr19:39921167-39922290	SK-N-SH	brain:	n/a	chr19:39921458-39921466 chr19:39921457-39921466 chr19:39921456-39921467 chr19:39921454-39921465 chr19:39921459-39921466 chr19:39921458-39921467
14	POLR2A	chr19:39921168-39927547	K562	blood:	n/a	n/a
15	POLR2A	chr19:39920942-39925617	GM12892	blood:	n/a	n/a
16	POLR2A	chr19:39920975-39927064	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
18	FOSL2	chr19:39920935-39922296	A549	lung:	n/a	chr19:39921458-39921466 chr19:39921457-39921466 chr19:39921454-39921465 chr19:39921459-39921466 chr19:39921458-39921467
19	POLR2A	chr19:39920712-39925660	IMR90	lung:	n/a	n/a
20	POLR2A	chr19:39921015-39927381	Hela-S3	cervix:	n/a	n/a
21	ATF2	chr19:39921223-39922397	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:39921127-39925489	GM12892	blood:	n/a	n/a
23	POLR2A	chr19:39921140-39922486	GM12878	blood:	n/a	n/a
24	PML	chr19:39921095-39922381	GM12878	blood:	n/a	chr19:39921459-39921468
25	POLR2A	chr19:39921043-39927658	HCT-116	colon:	n/a	n/a
26	POLR2A	chr19:39920992-39925485	GM12891	blood:	n/a	n/a
27	REST	chr19:39920516-39925106	PANC-1	pancreas:	n/a	chr19:39924867-39924880
28	POLR2A	chr19:39921505-39922385	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:39921169-39925654	K562	blood:	n/a	n/a
30	BCL3	chr19:39920999-39922359	A549	lung:	n/a	chr19:39921457-39921466 chr19:39921458-39921467
31	TCF12	chr19:39920831-39922400	A549	lung:	n/a	chr19:39921368-39921375
32	POLR2A	chr19:39921059-39925766	H1-hESC	embryonic stem cell:	n/a	n/a
33	SIX5	chr19:39920908-39927672	A549	lung:	n/a	chr19:39927463-39927477
34	POLR2A	chr19:39921027-39924615	A549	lung:	n/a	n/a
35	REST	chr19:39921048-39922344	A549	lung:	n/a	n/a
36	POLR2A	chr19:39922212-39922331	A549	lung:	n/a	n/a
37	SIN3AK20	chr19:39921040-39922316	A549	lung:	n/a	n/a
38	POLR2A	chr19:39921190-39922301	K562	blood:	n/a	n/a
39	POLR2A	chr19:39921064-39925450	HUVEC	blood vessel:	n/a	n/a
40	BCL3	chr19:39920896-39922420	A549	lung:	n/a	chr19:39921457-39921466 chr19:39921458-39921467
41	ZNF384	chr19:39922212-39922494	K562	blood:	n/a	n/a
42	GATA3	chr19:39921025-39922334	A549	lung:	n/a	chr19:39921456-39921465
43	ELF1	chr19:39921451-39922483	GM12878	blood:	n/a	n/a
44	NFATC1	chr19:39921344-39922307	GM12878	blood:	n/a	n/a
45	NR2F2	chr19:39921938-39922313	K562	blood:	n/a	n/a
46	POLR2A	chr19:39921143-39925465	GM12878	blood:	n/a	n/a
47	BCLAF1	chr19:39921319-39922364	GM12878	blood:	n/a	chr19:39921457-39921466 chr19:39921458-39921467
48	NFATC1	chr19:39921090-39922294	GM12878	blood:	n/a	n/a
49	RUNX3	chr19:39921245-39922313	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:39921326-39922331	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39921832..39923691-chr19:39996313..39998056,2	K562	blood:
2	chr19:39921621..39923975-chr19:39932520..39935648,3	MCF-7	breast:
3	chr19:39915714..39918595-chr19:39919774..39922739,3	MCF-7	breast:
4	chr19:39921200..39923671-chr19:40028899..40031832,2	K562	blood:
5	chr19:39921622..39923186-chr19:39964925..39966961,2	K562	blood:
6	chr19:39922266..39923824-chr19:39949808..39952006,2	K562	blood:
7	chr1:17231264..17231878-chr19:39921645..39922367,2	Hela-S3	cervix:

Variant related genes	Relation type
SUPT5H	TF binding region
ENSG00000269410	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000272426	Chromatin interaction
ENSG00000176396	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs57689442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61639559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61676286	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
3	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
5	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
7	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
9	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
10	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39904800-39925800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39905400-39923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:39905800-39923000	Weak transcription	Brain Anterior Caudate	brain
4	chr19:39905800-39923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:39910000-39922600	Weak transcription	Liver	Liver
6	chr19:39911400-39923400	Weak transcription	Fetal Brain Male	brain
7	chr19:39913800-39922800	Weak transcription	Psoas Muscle	Psoas
8	chr19:39915400-39923000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:39916800-39923000	Weak transcription	Dnd41	blood
10	chr19:39917400-39922800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:39917400-39923000	Weak transcription	Brain Angular Gyrus	brain
12	chr19:39917400-39923000	Weak transcription	Brain Substantia Nigra	brain
13	chr19:39919600-39923000	Weak transcription	Pancreas	Pancrea
14	chr19:39919600-39923200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:39919600-39925000	Weak transcription	Right Atrium	heart
16	chr19:39919800-39922800	Weak transcription	Fetal Intestine Large	intestine
17	chr19:39919800-39923000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:39919800-39923000	Weak transcription	Left Ventricle	heart
19	chr19:39919800-39923200	Weak transcription	HMEC	breast
20	chr19:39919800-39923600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:39919800-39923600	Weak transcription	Fetal Kidney	kidney
22	chr19:39919800-39924800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr19:39920000-39922800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:39920000-39923000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:39920000-39923000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:39920000-39923000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr19:39920000-39923000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:39920000-39923000	Weak transcription	HSMMtube	muscle
29	chr19:39920000-39923200	Weak transcription	Ovary	ovary
30	chr19:39920000-39923400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:39920000-39923400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:39920000-39924200	Weak transcription	Fetal Heart	heart
33	chr19:39920200-39923200	Weak transcription	Fetal Lung	lung
34	chr19:39921000-39922600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:39921200-39924600	Strong transcription	Brain Germinal Matrix	brain
36	chr19:39921200-39924800	Strong transcription	Brain Hippocampus Middle	brain
37	chr19:39921400-39922400	Strong transcription	Fetal Brain Female	brain
38	chr19:39921400-39923200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr19:39921400-39924200	Strong transcription	Colon Smooth Muscle	Colon
40	chr19:39921600-39922400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:39921600-39924200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:39921600-39924800	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr19:39921600-39925200	Strong transcription	Thymus	Thymus
44	chr19:39921600-39925600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:39921800-39922600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr19:39921800-39922600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:39921800-39922800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:39921800-39923200	Weak transcription	NHLF	lung
49	chr19:39921800-39923400	Weak transcription	Primary B cells from cord blood	blood
50	chr19:39921800-39923600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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