Variant report

Variant	rs9890510
Chromosome Location	chr17:46725149-46725150
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	IRF1	chr17:46724846-46725269	K562	blood:	n/a	chr17:46725053-46725067 chr17:46725052-46725065 chr17:46725051-46725058 chr17:46725053-46725063 chr17:46725049-46725063 chr17:46725047-46725064 chr17:46725052-46725065 chr17:46725052-46725064 chr17:46725051-46725071 chr17:46725049-46725066 chr17:46725052-46725066 chr17:46725051-46725065 chr17:46725052-46725063 chr17:46725052-46725065
2	CTCF	chr17:46725000-46725150	GM12872	blood:	n/a	n/a
3	SP1	chr17:46723866-46725210	A549	lung:	n/a	chr17:46724741-46724753 chr17:46724707-46724721 chr17:46724742-46724751 chr17:46724710-46724722 chr17:46724741-46724753 chr17:46724710-46724722
4	BCL3	chr17:46724493-46725326	A549	lung:	n/a	chr17:46725054-46725063 chr17:46724845-46724858
5	POLR2A	chr17:46722530-46725520	PANC-1	pancreas:	n/a	n/a
6	IRF1	chr17:46724918-46725165	K562	blood:	n/a	chr17:46725053-46725067 chr17:46725052-46725065 chr17:46725051-46725058 chr17:46725053-46725063 chr17:46725049-46725063 chr17:46725047-46725064 chr17:46725052-46725065 chr17:46725052-46725064 chr17:46725051-46725071 chr17:46725049-46725066 chr17:46725052-46725066 chr17:46725051-46725065 chr17:46725052-46725063 chr17:46725052-46725065
7	POLR2A	chr17:46724628-46725250	K562	blood:	n/a	n/a
8	MAX	chr17:46722708-46725666	A549	lung:	n/a	chr17:46723121-46723130 chr17:46723879-46723888 chr17:46724711-46724721 chr17:46722824-46722834 chr17:46725236-46725246
9	RCOR1	chr17:46725121-46725494	K562	blood:	n/a	n/a
10	ESRRA	chr17:46723585-46725678	GM12878	blood:	n/a	chr17:46725253-46725266 chr17:46724752-46724765
11	POLR2A	chr17:46724799-46725165	K562	blood:	n/a	n/a
12	ZNF143	chr17:46724834-46725521	H1-hESC	embryonic stem cell:	n/a	n/a
13	TEAD4	chr17:46724814-46725237	K562	blood:	n/a	n/a
14	CBX3	chr17:46725098-46725526	K562	blood:	n/a	n/a
15	POLR2A	chr17:46723212-46725478	HCT-116	colon:	n/a	n/a
16	MAX	chr17:46722803-46725460	A549	lung:	n/a	chr17:46723121-46723130 chr17:46723879-46723888 chr17:46724711-46724721 chr17:46722824-46722834 chr17:46725236-46725246
17	POLR2A	chr17:46723668-46725261	GM19099	blood:	n/a	n/a
18	CTCF	chr17:46725060-46725210	AG10803	skin:	n/a	n/a
19	TCF12	chr17:46722658-46725526	A549	lung:	n/a	chr17:46725205-46725213 chr17:46723577-46723585
20	POLR2A	chr17:46721618-46725581	PANC-1	pancreas:	n/a	n/a
21	CTCF	chr17:46725060-46725210	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000272763	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12941331	0.85[YRI][hapmap]
rs55682497	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55786154	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56314407	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212669	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs72829893	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72829895	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72829897	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72829902	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831805	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831816	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831822	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72831824	0.86[EUR][1000 genomes]
rs72831829	0.86[EUR][1000 genomes]
rs72831830	0.84[EUR][1000 genomes]
rs9893432	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
2	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
3	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
4	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
5	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
6	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
7	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	356 gene(s)	inside rSNPs	diseases
8	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46722000-46725400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:46722400-46725200	Active TSS	A549	lung
3	chr17:46722600-46725400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
4	chr17:46723000-46725400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr17:46723000-46725400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
6	chr17:46723400-46725200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr17:46723400-46725200	Bivalent/Poised TSS	HSMM	muscle
8	chr17:46723600-46725200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:46723600-46725200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
10	chr17:46723600-46725200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
11	chr17:46723600-46725400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr17:46723600-46725400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:46723600-46725400	Enhancers	Pancreas	Pancrea
14	chr17:46723800-46725200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
15	chr17:46724000-46725200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:46724000-46725200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
17	chr17:46724000-46725400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr17:46724400-46725400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
19	chr17:46724400-46725400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
20	chr17:46724600-46725200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:46724600-46725200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr17:46724600-46725200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr17:46724600-46725200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
25	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
26	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
27	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
32	chr17:46724600-46725200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
33	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
34	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
35	chr17:46724600-46725200	Bivalent/Poised TSS	Fetal Lung	lung
36	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
37	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
38	chr17:46724600-46725200	Flanking Active TSS	Ovary	ovary
39	chr17:46724600-46725200	Bivalent/Poised TSS	Psoas Muscle	Psoas
40	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
41	chr17:46724600-46725200	Bivalent/Poised TSS	Thymus	Thymus
42	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	HMEC	breast
43	chr17:46724600-46725200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr17:46724600-46725200	Bivalent/Poised TSS	NHLF	lung
45	chr17:46724600-46725400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr17:46724600-46725400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
47	chr17:46724600-46725400	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
48	chr17:46724600-46725400	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
49	chr17:46724600-46725400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr17:46724600-46725400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links