Variant report

Variant	rs141214200
Chromosome Location	chr19:38876184-38876185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38875977-38876597	A549	lung:	n/a	n/a
2	POLR2A	chr19:38876175-38876194	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:38875930-38876368	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:38874843-38876344	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr19:38874550-38877193	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr19:38874404-38876202	A549	lung:	n/a	chr19:38875535-38875551 chr19:38875529-38875550 chr19:38875534-38875552 chr19:38875536-38875549
7	POLR2A	chr19:38874762-38876307	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:38876045-38876220	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr19:38874034-38876600	K562	blood:	n/a	n/a
10	POLR2A	chr19:38871440-38886227	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr19:38874152-38877033	GM12891	blood:	n/a	n/a
12	POLR2A	chr19:38875909-38876348	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr19:38874035-38876338	K562	blood:	n/a	n/a
14	POLR2A	chr19:38874785-38879102	A549	lung:	n/a	n/a
15	POLR2A	chr19:38875922-38876325	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr19:38874623-38876880	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:38874823-38876241	GM12892	blood:	n/a	n/a
18	POLR2A	chr19:38869603-38879135	K562	blood:	n/a	n/a
19	POLR2A	chr19:38874605-38876529	K562	blood:	n/a	n/a
20	POLR2A	chr19:38875923-38876669	A549	lung:	n/a	n/a
21	POLR2A	chr19:38873616-38876905	A549	lung:	n/a	n/a
22	POLR2A	chr19:38874045-38876287	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:38876144-38876396	A549	lung:	n/a	n/a
24	POLR2A	chr19:38874705-38876483	HL-60	blood:	n/a	n/a
25	POLR2A	chr19:38874471-38877088	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr19:38873453-38879163	K562	blood:	n/a	n/a
27	POLR2A	chr19:38874175-38877146	GM12892	blood:	n/a	n/a
28	POLR2A	chr19:38873627-38879112	K562	blood:	n/a	n/a
29	POLR2A	chr19:38873798-38877126	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr19:38874901-38876812	GM19193	blood:	n/a	n/a
31	POLR2A	chr19:38874768-38876500	U87	brain:	n/a	n/a
32	BCL3	chr19:38874813-38876285	A549	lung:	n/a	n/a
33	POLR2A	chr19:38874068-38876982	GM12892	blood:	n/a	n/a
34	POLR2A	chr19:38874772-38877051	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:38874370-38877112	HepG2	liver:	n/a	n/a
36	POLR2A	chr19:38873479-38877165	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:38873532-38876808	GM12892	blood:	n/a	n/a
38	POLR2A	chr19:38873689-38876797	HepG2	liver:	n/a	n/a
39	POLR2A	chr19:38875768-38876439	U87	brain:	n/a	n/a
40	POLR2A	chr19:38873576-38876991	PANC-1	pancreas:	n/a	n/a
41	POLR2A	chr19:38874921-38876322	ECC-1	luminal epithelium:	n/a	n/a
42	HMGN3	chr19:38876003-38876440	K562	blood:	n/a	n/a
43	POLR2A	chr19:38874774-38876409	U87	brain:	n/a	n/a
44	POLR2A	chr19:38873583-38876671	K562	blood:	n/a	n/a
45	POLR2A	chr19:38875994-38876240	MCF-7	breast:	n/a	n/a
46	POLR2A	chr19:38874801-38877095	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:38876160-38876210	GM06990	blood:	n/a
2	chr19:38876160-38876210	IMR90	lung:	fetal
3	chr19:38876160-38876210	AoSMC	blood vessel:	n/a
4	chr19:38876160-38876210	PFSK-1	brain:	n/a
5	chr19:38876160-38876210	T-47D	breast:	n/a
6	chr19:38876160-38876210	Jurkat	blood:	n/a
7	chr19:38876160-38876210	HAEpiC	amniotic membrane:	n/a
8	chr19:38876160-38876210	ProgFib	skin:	n/a
9	chr19:38876160-38876210	K562	blood:	n/a
10	chr19:38876160-38876210	NHBE	bronchial:	n/a
11	chr19:38876160-38876210	HCT-116	colon:	n/a
12	chr19:38876160-38876210	NB4	blood:	n/a
13	chr19:38876160-38876210	AG09309	skin:	n/a
14	chr19:38876160-38876210	GM19239	blood:	n/a
15	chr19:38876160-38876210	HMEC	breast:	n/a
16	chr19:38876160-38876210	U87	brain:	n/a
17	chr19:38876160-38876210	MCF10A-Er-Src	breast:	n/a
18	chr19:38876160-38876210	PANC-1	pancreas:	n/a
19	chr19:38876160-38876210	GM12878	blood:	n/a
20	chr19:38876160-38876210	AG04450	lung:	fetal
21	chr19:38876160-38876210	HL-60	blood:	n/a
22	chr19:38876160-38876210	SK-N-MC	brain:	n/a
23	chr19:38876160-38876210	SK-N-SH	brain:	n/a
24	chr19:38876160-38876210	GM12892	blood:	n/a
25	chr19:38876160-38876210	ECC-1	luminal epithelium:	n/a
26	chr19:38876160-38876210	SKMC	muscle:	n/a
27	chr19:38876160-38876210	HNPCEpiC	eye:	n/a
28	chr19:38876160-38876210	HCPEpiC	choroid plexus:	n/a
29	chr19:38876160-38876210	Hela-S3	cervix:	n/a
30	chr19:38876160-38876210	HPAEpiC	pulmonary alveolar:	n/a
31	chr19:38876160-38876210	NHDF-neo	bronchial:	n/a
32	chr19:38876160-38876210	BJ	skin:	n/a
33	chr19:38876160-38876210	LNCaP	prostate:	n/a
34	chr19:38876160-38876210	HRPEpiC	eye:	n/a
35	chr19:38876160-38876210	HRE	kidney:	n/a
36	chr19:38876160-38876210	AG09319	gingival:	n/a
37	chr19:38876160-38876210	Hepatocyte	liver:	n/a
38	chr19:38876160-38876210	CMK	blood:	n/a
39	chr19:38876160-38876210	HUVEC	blood vessel:	n/a
40	chr19:38876160-38876210	SAEC	small airway:	n/a
41	chr19:38876160-38876210	HEK293	kidney:	embryo
42	chr19:38876160-38876210	NH-A	brain:	n/a
43	chr19:38876160-38876210	Caco-2	colon:	n/a
44	chr19:38876160-38876210	SK-N-SH_RA	brain:	n/a
45	chr19:38876160-38876210	NT2-D1	testis:	n/a
46	chr19:38876160-38876210	HepG2	liver:	n/a
47	chr19:38876160-38876210	HCM	heart:	n/a
48	chr19:38876160-38876210	MCF-7	breast:	n/a
49	chr19:38876160-38876210	RPTEC	kidney:	n/a
50	chr19:38876160-38876210	AG04449	skin:	fetal

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38876175..38878484-chr19:38901904..38903905,2	K562	blood:
2	chr19:38873942..38878444-chr19:38892255..38895006,5	K562	blood:
3	chr19:36630602..36632414-chr19:38875371..38878496,3	MCF-7	breast:
4	chr19:38719348..38721458-chr19:38874867..38876458,2	K562	blood:
5	chr19:38804471..38807313-chr19:38874109..38876554,2	MCF-7	breast:
6	chr19:38824957..38829265-chr19:38874295..38879043,8	MCF-7	breast:

No data

Variant related genes	Relation type
SPRED3	TF binding region
SPRED3	CpG island
ENSG00000130244	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000171777	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	esv3361438	chr19:38875337-38877885	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38867000-38877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38867000-38878000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:38867200-38877000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:38867200-38877200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:38867200-38877400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:38867600-38876200	Strong transcription	Brain Cingulate Gyrus	brain
7	chr19:38867600-38877400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:38867800-38876200	Strong transcription	Adipose Nuclei	Adipose
9	chr19:38867800-38876200	Strong transcription	Brain Hippocampus Middle	brain
10	chr19:38867800-38876600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:38867800-38877000	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr19:38868000-38876200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:38868000-38877600	Weak transcription	Right Atrium	heart
14	chr19:38868400-38876400	Strong transcription	Colonic Mucosa	Colon
15	chr19:38869400-38876400	Strong transcription	HMEC	breast
16	chr19:38869600-38876200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:38869600-38876400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:38869600-38876600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:38869600-38877400	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:38869600-38877800	Strong transcription	NHLF	lung
21	chr19:38869800-38876200	Strong transcription	Brain Substantia Nigra	brain
22	chr19:38869800-38876200	Strong transcription	Pancreas	Pancrea
23	chr19:38870200-38876200	Strong transcription	Right Ventricle	heart
24	chr19:38870200-38877400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:38870400-38876800	Strong transcription	Ovary	ovary
26	chr19:38873000-38876400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:38873000-38876400	Genic enhancers	Placenta	Placenta
28	chr19:38873000-38877800	Weak transcription	Hela-S3	cervix
29	chr19:38873200-38877600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:38873600-38876200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
31	chr19:38874000-38876200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:38874000-38876600	Strong transcription	Esophagus	oesophagus
33	chr19:38874000-38877600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr19:38874200-38876200	Strong transcription	NHEK	skin
35	chr19:38874200-38876400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:38874200-38876400	Strong transcription	Lung	lung
37	chr19:38874400-38876200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr19:38874400-38876400	Weak transcription	Primary B cells from cord blood	blood
39	chr19:38874400-38877600	Weak transcription	HUVEC	blood vessel
40	chr19:38874600-38876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:38874600-38877200	Weak transcription	NH-A	brain
42	chr19:38874600-38877800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr19:38874800-38876200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:38874800-38876400	Genic enhancers	Dnd41	blood
45	chr19:38874800-38876600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr19:38874800-38876800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:38874800-38876800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr19:38874800-38877000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:38874800-38877200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:38874800-38877200	Weak transcription	NHDF-Ad	bronchial

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