Variant report

Variant	rs13058399
Chromosome Location	chr22:30694428-30694429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:59)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:59 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr22:30694241-30694653	T-47D	breast:	n/a	n/a
2	CTCF	chr22:30694280-30694430	HEK293	kidney:	n/a	n/a
3	MAX	chr22:30694015-30694960	MCF-7	breast:	n/a	n/a
4	CTCF	chr22:30694343-30694538	LNCaP	prostate:	n/a	n/a
5	NR2F2	chr22:30694162-30694774	MCF-7	breast:	n/a	n/a
6	MYC	chr22:30694264-30694636	MCF-7	breast:	n/a	n/a
7	ESR1	chr22:30694353-30694614	ECC-1	luminal epithelium:	n/a	n/a
8	FOXA1	chr22:30694284-30694679	ECC-1	luminal epithelium:	n/a	n/a
9	FOXA1	chr22:30694363-30694706	ECC-1	luminal epithelium:	n/a	n/a
10	MYC	chr22:30694294-30694554	MCF-7	breast:	n/a	n/a
11	ESR1	chr22:30694297-30694634	T-47D	breast:	n/a	n/a
12	ZNF217	chr22:30694287-30694859	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr22:30694036-30694913	MCF-7	breast:	n/a	n/a
14	HDAC2	chr22:30694251-30694814	MCF-7	breast:	n/a	n/a
15	NR2F2	chr22:30694219-30695078	MCF-7	breast:	n/a	n/a
16	ESR1	chr22:30694270-30694693	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr22:30694382-30694543	NHEK	skin:	n/a	n/a
18	CTCF	chr22:30694360-30694510	Caco-2	colon:	n/a	n/a
19	GATA3	chr22:30694273-30694840	MCF-7	breast:	n/a	n/a
20	CTCF	chr22:30694340-30694490	HEEpiC	esophagus:	n/a	n/a
21	ELF1	chr22:30694175-30694856	MCF-7	breast:	n/a	n/a
22	CTCF	chr22:30694343-30694551	MCF-7	breast:	n/a	n/a
23	ESR1	chr22:30694274-30694623	T-47D	breast:	n/a	n/a
24	FOSL2	chr22:30694225-30694796	MCF-7	breast:	n/a	n/a
25	GATA3	chr22:30694332-30694710	T-47D	breast:	n/a	n/a
26	CTCF	chr22:30694320-30694470	BE2_C	brain:	n/a	n/a
27	RAD21	chr22:30694226-30694733	MCF-7	breast:	n/a	n/a
28	CTCF	chr22:30694400-30694550	HMEC	breast:	n/a	n/a
29	FOXA1	chr22:30694239-30694705	T-47D	breast:	n/a	n/a
30	MAX	chr22:30694231-30694790	ECC-1	luminal epithelium:	n/a	n/a
31	EP300	chr22:30694267-30694742	T-47D	breast:	n/a	n/a
32	CTCF	chr22:30694349-30694515	MCF-7	breast:	n/a	n/a
33	CTCF	chr22:30694360-30694510	HMEC	breast:	n/a	n/a
34	CTCF	chr22:30694420-30694570	SAEC	small airway:	n/a	n/a
35	CTCF	chr22:30694420-30694570	NHEK	skin:	n/a	n/a
36	CTCF	chr22:30694222-30694759	MCF-7	breast:	n/a	n/a
37	RAD21	chr22:30694153-30694880	MCF-7	breast:	n/a	n/a
38	GATA3	chr22:30694178-30694949	MCF-7	breast:	n/a	n/a
39	EP300	chr22:30694332-30694748	MCF-7	breast:	n/a	n/a
40	CTCF	chr22:30694382-30694556	LNCaP	prostate:	n/a	n/a
41	MYC	chr22:30694083-30694680	MCF-7	breast:	n/a	n/a
42	MAX	chr22:30694070-30694856	MCF-7	breast:	n/a	n/a
43	SIN3AK20	chr22:30694110-30694995	MCF-7	breast:	n/a	n/a
44	HDAC2	chr22:30694158-30694924	MCF-7	breast:	n/a	n/a
45	MAX	chr22:30694180-30694731	ECC-1	luminal epithelium:	n/a	n/a
46	FOXA1	chr22:30694307-30694723	T-47D	breast:	n/a	n/a
47	CTCF	chr22:30694345-30694518	MCF-7	breast:	n/a	n/a
48	CTCF	chr22:30694380-30694530	SAEC	small airway:	n/a	n/a
49	ESR1	chr22:30694234-30694674	ECC-1	luminal epithelium:	n/a	n/a
50	EP300	chr22:30694191-30694852	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30683550..30684480-chr22:30694057..30694832,4	MCF-7	breast:
2	chr22:30692849..30696422-chr22:30721996..30724187,4	MCF-7	breast:
3	chr22:30692983..30695862-chr22:30751814..30754169,4	MCF-7	breast:
4	chr22:30692354..30698688-chr22:30699927..30704803,9	K562	blood:
5	chr22:30692473..30695111-chr22:30722676..30724964,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000248751	TF binding region
TBC1D10A	TF binding region
ENSG00000099992	Chromatin interaction
ENSG00000239282	Chromatin interaction
ENSG00000187860	Chromatin interaction
ENSG00000099995	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13056562	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058084	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058535	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17730748	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738020	1.00[ASW][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs34102711	1.00[ASN][1000 genomes]
rs34318316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911581	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34964064	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35074129	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35246430	1.00[ASN][1000 genomes]
rs35617977	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35960997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449240	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4820002	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820834	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823086	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823087	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67401267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73168654	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv1799458	chr22:30659798-30698035	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13058399	LOC200312	cis	multi-tissue	Pritchard
rs13058399	RP1-130H16.16	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30686000-30700000	Weak transcription	Fetal Kidney	kidney
2	chr22:30686200-30720000	Weak transcription	Fetal Brain Male	brain
3	chr22:30686400-30701800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr22:30686600-30700600	Genic enhancers	Fetal Thymus	thymus
5	chr22:30686800-30694800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr22:30686800-30701800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr22:30686800-30707200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr22:30687000-30695800	Strong transcription	Brain Germinal Matrix	brain
9	chr22:30687000-30699600	Strong transcription	Fetal Brain Female	brain
10	chr22:30687200-30697200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr22:30687400-30695200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr22:30687400-30695800	Strong transcription	Primary B cells from cord blood	blood
13	chr22:30687400-30696400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr22:30687400-30696600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr22:30687400-30701200	Weak transcription	K562	blood
16	chr22:30687400-30706800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr22:30687600-30694600	Strong transcription	Fetal Intestine Small	intestine
18	chr22:30687600-30695600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr22:30687600-30696400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr22:30687600-30697200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr22:30687600-30699000	Weak transcription	HepG2	liver
22	chr22:30687600-30699800	Genic enhancers	Esophagus	oesophagus
23	chr22:30687600-30701400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr22:30687800-30696400	Weak transcription	NHDF-Ad	bronchial
25	chr22:30687800-30696600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr22:30687800-30697600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr22:30687800-30698000	Strong transcription	Osteobl	bone
28	chr22:30688000-30697400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr22:30688000-30697400	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr22:30688000-30697600	Weak transcription	HUVEC	blood vessel
31	chr22:30688200-30696400	Strong transcription	Adipose Nuclei	Adipose
32	chr22:30688200-30696800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr22:30688200-30697200	Weak transcription	Brain Angular Gyrus	brain
34	chr22:30688200-30697200	Strong transcription	HSMMtube	muscle
35	chr22:30688200-30697800	Strong transcription	NHLF	lung
36	chr22:30688200-30698400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr22:30688200-30698600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr22:30688200-30699200	Strong transcription	Aorta	Aorta
39	chr22:30688200-30700600	Strong transcription	Fetal Stomach	stomach
40	chr22:30688400-30694800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr22:30688400-30695000	Strong transcription	Brain Anterior Caudate	brain
42	chr22:30688400-30696800	Strong transcription	Fetal Muscle Leg	muscle
43	chr22:30688400-30697400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr22:30688400-30697800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr22:30688400-30697800	Strong transcription	Liver	Liver
46	chr22:30688400-30698000	Strong transcription	GM12878-XiMat	blood
47	chr22:30688600-30697800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr22:30688800-30696200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr22:30689600-30695200	Genic enhancers	Thymus	Thymus
50	chr22:30689800-30698200	Weak transcription	A549	lung

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