Variant report

Variant	rs7022475
Chromosome Location	chr9:99983931-99983932
allele	G/T
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	CTCF	chr9:99983856-99983993	MCF-7	breast:	n/a	chr9:99983926-99983944
2	CTCF	chr9:99983918-99983964	Kidney_OC	kidney:	n/a	chr9:99983926-99983944
3	MAX	chr9:99983744-99984141	ECC-1	luminal epithelium:	n/a	n/a
4	RXRA	chr9:99983897-99985209	HepG2	liver:	n/a	chr9:99984890-99984897 chr9:99983926-99983946 chr9:99983934-99983941
5	CTCF	chr9:99983880-99984030	HAc	cerebellar:	n/a	chr9:99983926-99983944
6	MAX	chr9:99983425-99983958	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr9:99983873-99985026	A549	lung:	n/a	n/a
8	CTCF	chr9:99983900-99984050	HA-sp	spinal cord:	n/a	chr9:99983926-99983944
9	MAX	chr9:99983721-99984208	A549	lung:	n/a	n/a
10	POLR2A	chr9:99983796-99985202	GM12892	blood:	n/a	n/a
11	TAF7	chr9:99982017-99985169	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF3	chr9:99983672-99985117	GM12878	blood:	n/a	chr9:99984987-99985000 chr9:99984815-99984828 chr9:99985016-99985029 chr9:99984442-99984455
13	CTCF	chr9:99983900-99984050	A549	lung:	n/a	chr9:99983926-99983944
14	RAD21	chr9:99983839-99984036	HepG2	liver:	n/a	chr9:99983930-99983943
15	RAD21	chr9:99983823-99983984	K562	blood:	n/a	chr9:99983930-99983943
16	CTCF	chr9:99983840-99983990	HUVEC	blood vessel:	n/a	chr9:99983926-99983944
17	HA-E2F1	chr9:99983643-99984527	MCF-7	breast:	n/a	chr9:99984427-99984439 chr9:99983954-99983963 chr9:99983956-99983966 chr9:99984152-99984162
18	CTCF	chr9:99983879-99984000	NHEK	skin:	n/a	chr9:99983926-99983944
19	CTCF	chr9:99983900-99984050	HVMF	connective:	n/a	chr9:99983926-99983944
20	CBX3	chr9:99983628-99983965	K562	blood:	n/a	n/a
21	MAX	chr9:99983807-99984143	A549	lung:	n/a	n/a
22	CTCF	chr9:99983840-99983990	HCPEpiC	choroid plexus:	n/a	chr9:99983926-99983944
23	ATF2	chr9:99981818-99984334	H1-hESC	embryonic stem cell:	n/a	n/a
24	POU2F2	chr9:99983866-99985220	GM12878	blood:	n/a	chr9:99984669-99984681
25	POLR2A	chr9:99983630-99985202	GM12892	blood:	n/a	n/a
26	CTCF	chr9:99983857-99984007	MCF-7	breast:	n/a	chr9:99983926-99983944
27	ZNF263	chr9:99983682-99984320	HEK293-T-REx	kidney:	n/a	n/a
28	CTCF	chr9:99983800-99983950	AG04449	skin:	n/a	chr9:99983926-99983944
29	HCFC1	chr9:99983816-99983958	K562	blood:	n/a	n/a
30	CTCF	chr9:99983858-99983984	Pancreas_OC	pancreas:	n/a	chr9:99983926-99983944
31	MAX	chr9:99983727-99984027	ECC-1	luminal epithelium:	n/a	n/a
32	BHLHE40	chr9:99983908-99984108	K562	blood:	n/a	n/a
33	CTCF	chr9:99983880-99984030	HVMF	connective:	n/a	chr9:99983926-99983944
34	USF2	chr9:99983092-99984014	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr9:99983866-99983985	Lung_OC	lung:	n/a	chr9:99983926-99983944
36	HMGN3	chr9:99983788-99984099	K562	blood:	n/a	n/a
37	CTCF	chr9:99983892-99983984	LNCaP	prostate:	n/a	chr9:99983926-99983944
38	POLR2A	chr9:99982734-99985190	H1-hESC	embryonic stem cell:	n/a	n/a
39	TAF7	chr9:99982997-99984233	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr9:99982695-99985179	H1-hESC	embryonic stem cell:	n/a	n/a
41	UBTF	chr9:99983764-99984350	K562	blood:	n/a	n/a
42	GABPA	chr9:99983677-99984217	MCF-7	breast:	n/a	n/a
43	CTCF	chr9:99983781-99984367	A549	lung:	n/a	chr9:99983926-99983944 chr9:99984090-99984103 chr9:99984341-99984354
44	CTCF	chr9:99983820-99983970	WERI-Rb-1	eye:	n/a	chr9:99983926-99983944
45	BACH1	chr9:99983272-99983972	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr9:99983880-99984030	BJ	skin:	n/a	chr9:99983926-99983944
47	POLR2A	chr9:99981626-99985169	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr9:99983800-99983950	SAEC	small airway:	n/a	chr9:99983926-99983944
49	CHD2	chr9:99983890-99984012	K562	blood:	n/a	n/a
50	TEAD4	chr9:99983482-99984020	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:99983881..99984841-chr9:100149024..100149576,2	MCF-7	breast:

Variant related genes	Relation type
ANKRD18CP	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10116019	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119245	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759522	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817265	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10981209	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10981280	0.82[EUR][1000 genomes]
rs10981288	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10981296	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10981329	0.80[EUR][1000 genomes]
rs11562326	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11794422	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11998999	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12004930	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12235734	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13297670	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13298346	0.80[EUR][1000 genomes]
rs13299029	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28846196	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34382632	0.80[EUR][1000 genomes]
rs3957904	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3994556	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4284138	0.80[EUR][1000 genomes]
rs4626726	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55694850	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6478020	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7039446	0.87[ASN][1000 genomes]
rs7850392	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7850429	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7850504	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855366	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7855622	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868440	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7868563	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7868806	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869509	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869568	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7869587	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869959	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893607	chr9:99906545-99996548	Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7022475	ANKRD18CP	cis	Thyroid	GTEx
rs7022475	VN1R51P	cis	Thyroid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99976600-99985000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr9:99976600-99985000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr9:99976800-99985200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr9:99976800-99985400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr9:99981400-99985000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr9:99981800-99985000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr9:99982000-99985000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr9:99982000-99985200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:99982200-99985200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr9:99982400-99985200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:99983000-99984000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:99983000-99984400	Bivalent/Poised TSS	NHEK	skin
13	chr9:99983000-99984800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:99983000-99985000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr9:99983000-99985000	Active TSS	Brain Anterior Caudate	brain
16	chr9:99983000-99985200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr9:99983000-99985200	Bivalent Enhancer	Fetal Brain Male	brain
18	chr9:99983200-99984000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:99983200-99984000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:99983200-99984000	Enhancers	Spleen	Spleen
21	chr9:99983200-99984200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr9:99983200-99984200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:99983200-99984200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr9:99983200-99984200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
25	chr9:99983200-99984400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
26	chr9:99983200-99984400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
27	chr9:99983200-99984400	Bivalent Enhancer	Fetal Stomach	stomach
28	chr9:99983200-99984400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
29	chr9:99983200-99984400	Flanking Bivalent TSS/Enh	HMEC	breast
30	chr9:99983200-99984400	Bivalent/Poised TSS	HSMM	muscle
31	chr9:99983200-99984600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:99983200-99984600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
33	chr9:99983200-99984600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:99983200-99984600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
35	chr9:99983200-99984600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:99983200-99984600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:99983200-99984600	Bivalent Enhancer	Placenta	Placenta
38	chr9:99983200-99984600	Enhancers	Gastric	stomach
39	chr9:99983200-99984800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:99983200-99984800	Flanking Active TSS	Right Ventricle	heart
41	chr9:99983200-99985000	Enhancers	Lung	lung
42	chr9:99983200-99985200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:99983400-99984000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
44	chr9:99983400-99984200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:99983400-99984200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:99983400-99984200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
47	chr9:99983400-99984200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
48	chr9:99983400-99984200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
49	chr9:99983400-99984200	Flanking Active TSS	Liver	Liver
50	chr9:99983400-99984200	Bivalent/Poised TSS	Fetal Brain Female	brain

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