Variant report

Variant	rs7248778
Chromosome Location	chr19:52223121-52223122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr19:52222345-52223207	H1-hESC	embryonic stem cell:	n/a	n/a
2	GABPA	chr19:52222678-52223198	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr19:52222363-52223154	H1-hESC	embryonic stem cell:	n/a	chr19:52222371-52222380
4	MAX	chr19:52222422-52223207	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr19:52222330-52223294	H1-hESC	embryonic stem cell:	n/a	chr19:52222371-52222380
6	SIN3A	chr19:52222651-52223203	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52223099-52223149	HEK293	kidney:	embryo
2	chr19:52223099-52223149	IMR90	lung:	fetal
3	chr19:52223099-52223149	Caco-2	colon:	n/a
4	chr19:52223099-52223149	GM19239	blood:	n/a
5	chr19:52223099-52223149	GM06990	blood:	n/a
6	chr19:52223099-52223149	PFSK-1	brain:	n/a
7	chr19:52223099-52223149	U87	brain:	n/a
8	chr19:52223099-52223149	SK-N-MC	brain:	n/a
9	chr19:52223099-52223149	H1-hESC	embryonic stem cell:	embryo
10	chr19:52223099-52223149	SK-N-SH_RA	brain:	n/a
11	chr19:52223099-52223149	T-47D	breast:	n/a
12	chr19:52223099-52223149	RPTEC	kidney:	n/a
13	chr19:52223099-52223149	NB4	blood:	n/a
14	chr19:52223099-52223149	HL-60	blood:	n/a
15	chr19:52223099-52223149	HCT-116	colon:	n/a
16	chr19:52223099-52223149	AG09319	gingival:	n/a
17	chr19:52223099-52223149	NH-A	brain:	n/a
18	chr19:52223099-52223149	GM12892	blood:	n/a
19	chr19:52223099-52223149	PANC-1	pancreas:	n/a
20	chr19:52223099-52223149	NT2-D1	testis:	n/a
21	chr19:52223099-52223149	AG09309	skin:	n/a
22	chr19:52223099-52223149	HIPEpiC	eye:	n/a
23	chr19:52223099-52223149	PrEC	prostate:	n/a
24	chr19:52223099-52223149	MCF10A-Er-Src	breast:	n/a
25	chr19:52223099-52223149	ovcar-3	ovarian:	n/a
26	chr19:52223099-52223149	Hela-S3	cervix:	n/a
27	chr19:52223099-52223149	NHBE	bronchial:	n/a
28	chr19:52223099-52223149	HEEpiC	esophagus:	n/a
29	chr19:52223099-52223149	SK-N-SH	brain:	n/a
30	chr19:52223099-52223149	HCPEpiC	choroid plexus:	n/a
31	chr19:52223099-52223149	LNCaP	prostate:	n/a
32	chr19:52223099-52223149	A549	lung:	n/a
33	chr19:52223099-52223149	ProgFib	skin:	n/a
34	chr19:52223099-52223149	AG04450	lung:	fetal
35	chr19:52223099-52223149	AoSMC	blood vessel:	n/a
36	chr19:52223099-52223149	K562	blood:	n/a
37	chr19:52223099-52223149	HAEpiC	amniotic membrane:	n/a
38	chr19:52223099-52223149	HPAEpiC	pulmonary alveolar:	n/a
39	chr19:52223099-52223149	Hepatocyte	liver:	n/a
40	chr19:52223099-52223149	HUVEC	blood vessel:	n/a
41	chr19:52223099-52223149	HMEC	breast:	n/a
42	chr19:52223099-52223149	GM12891	blood:	n/a
43	chr19:52223099-52223149	HRE	kidney:	n/a
44	chr19:52223099-52223149	NHDF-neo	bronchial:	n/a
45	chr19:52223099-52223149	HepG2	liver:	n/a
46	chr19:52223099-52223149	Jurkat	blood:	n/a
47	chr19:52223099-52223149	CMK	blood:	n/a
48	chr19:52223099-52223149	AG10803	skin:	n/a
49	chr19:52223099-52223149	HCM	heart:	n/a
50	chr19:52223099-52223149	BJ	skin:	n/a

No data

Variant related genes	Relation type
HAS1	TF binding region
HAS1	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10417548	0.87[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084109	0.87[TSI][hapmap]
rs11084113	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667949	0.90[TSI][hapmap];0.83[AFR][1000 genomes]
rs11672222	0.88[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551155	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802854	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802855	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802856	0.84[TSI][hapmap]
rs57088533	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7252616	1.00[ASN][1000 genomes]
rs7259578	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
2	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
3	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
4	nsv1064914	chr19:52103914-52231564	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	529 gene(s)	inside rSNPs	diseases
5	nsv544052	chr19:52103914-52271247	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	531 gene(s)	inside rSNPs	diseases
6	nsv1056825	chr19:52103914-52359815	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
7	nsv544053	chr19:52103914-52359815	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
8	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
9	nsv1066046	chr19:52147399-52271247	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
10	nsv544054	chr19:52147399-52271247	Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
11	nsv912296	chr19:52182363-52231032	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	518 gene(s)	inside rSNPs	diseases
12	nsv915725	chr19:52184488-52439676	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
13	nsv1059148	chr19:52211749-52359815	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv912297	chr19:52213743-52227066	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52222000-52223400	Active TSS	Brain Angular Gyrus	brain
2	chr19:52222000-52223600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:52222000-52223600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
4	chr19:52222200-52223400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:52222200-52223400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:52222200-52223400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr19:52222200-52223400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
8	chr19:52222200-52223600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
9	chr19:52222200-52223600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr19:52222200-52223600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr19:52222200-52223600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:52222200-52223600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
13	chr19:52222400-52223200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr19:52222400-52223200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:52222400-52223200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
16	chr19:52222400-52223200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr19:52222400-52223200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
18	chr19:52222400-52223200	Bivalent Enhancer	Placenta	Placenta
19	chr19:52222400-52223200	ZNF genes & repeats	Spleen	Spleen
20	chr19:52222400-52223400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr19:52222400-52223400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:52222400-52223400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
23	chr19:52222400-52223400	Active TSS	Brain Substantia Nigra	brain
24	chr19:52222400-52223400	Bivalent/Poised TSS	Fetal Brain Female	brain
25	chr19:52222400-52223600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
26	chr19:52222400-52223600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:52222400-52223600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:52222400-52224000	Active TSS	HSMM	muscle
29	chr19:52222600-52223200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:52222600-52223200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:52222600-52223200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:52222600-52223200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:52222600-52223200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:52222600-52223200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr19:52222600-52223200	Bivalent Enhancer	Esophagus	oesophagus
36	chr19:52222600-52223200	Bivalent Enhancer	Fetal Brain Male	brain
37	chr19:52222600-52223200	Bivalent Enhancer	Fetal Lung	lung
38	chr19:52222600-52223200	Bivalent Enhancer	Lung	lung
39	chr19:52222600-52223200	Enhancers	Pancreas	Pancrea
40	chr19:52222600-52223200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
41	chr19:52222600-52223200	Bivalent/Poised TSS	HSMMtube	muscle
42	chr19:52222600-52223400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:52222600-52223400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
44	chr19:52222600-52223400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:52222600-52223400	Bivalent/Poised TSS	Osteobl	bone
46	chr19:52222800-52223200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:52222800-52223200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
48	chr19:52222800-52223200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:52222800-52223200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:52222800-52223200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links