Variant report

Variant	rs2442373
Chromosome Location	chr13:39260130-39260131
allele	C/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	ZNF217	chr13:39260128-39260600	MCF-7	breast:	n/a	n/a
2	CTCF	chr13:39260120-39260270	NHLF	lung:	n/a	chr13:39260205-39260223
3	CTCF	chr13:39260080-39260230	GM12872	blood:	n/a	chr13:39260205-39260223
4	CTCF	chr13:39260060-39260210	MCF-7	breast:	n/a	n/a
5	ESR1	chr13:39260045-39260656	T-47D	breast:	n/a	n/a
6	RAD21	chr13:39260045-39260422	GM12878	blood:	n/a	n/a
7	RAD21	chr13:39260013-39260498	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr13:39260077-39260361	Medullo	brain:	n/a	chr13:39260205-39260223
9	CTCF	chr13:39260126-39260296	HepG2	liver:	n/a	chr13:39260205-39260223
10	CTCF	chr13:39260060-39260210	HMEC	breast:	n/a	n/a
11	EP300	chr13:39260084-39260714	T-47D	breast:	n/a	chr13:39260616-39260632
12	CTCF	chr13:39260113-39260152	Kidney_OC	kidney:	n/a	n/a
13	CTCF	chr13:39260120-39260270	GM12873	blood:	n/a	chr13:39260205-39260223
14	CTCF	chr13:39259975-39260442	MCF-7	breast:	n/a	chr13:39260205-39260223
15	RAD21	chr13:39259907-39260702	MCF-7	breast:	n/a	n/a
16	ESR1	chr13:39260091-39260632	T-47D	breast:	n/a	n/a
17	CTCF	chr13:39260120-39260270	WERI-Rb-1	eye:	n/a	chr13:39260205-39260223
18	ESR1	chr13:39260043-39260682	T-47D	breast:	n/a	n/a
19	CTCF	chr13:39260100-39260250	GM12878	blood:	n/a	chr13:39260205-39260223
20	SIN3AK20	chr13:39260053-39260966	MCF-7	breast:	n/a	n/a
21	CTCF	chr13:39260120-39260270	HCPEpiC	choroid plexus:	n/a	chr13:39260205-39260223
22	FOS	chr13:39260076-39260382	MCF10A-Er-Src	breast:	n/a	n/a
23	TEAD4	chr13:39260102-39260747	MCF-7	breast:	n/a	n/a
24	RAD21	chr13:39260029-39260720	MCF-7	breast:	n/a	n/a
25	CTCF	chr13:39260055-39260383	H1-hESC	embryonic stem cell:	n/a	chr13:39260205-39260223
26	RAD21	chr13:39260076-39260387	SK-N-SH_RA	brain:	n/a	n/a
27	FOXA1	chr13:39260088-39260730	T-47D	breast:	n/a	n/a
28	SIN3AK20	chr13:39259931-39261825	MCF-7	breast:	n/a	n/a
29	CTCF	chr13:39260126-39260327	MCF-7	breast:	n/a	chr13:39260205-39260223
30	CTCF	chr13:39260120-39260270	HRE	kidney:	n/a	chr13:39260205-39260223
31	CTCF	chr13:39260100-39260250	NHDF-neo	bronchial:	n/a	chr13:39260205-39260223
32	GATA3	chr13:39260044-39260728	T-47D	breast:	n/a	n/a
33	CTCF	chr13:39259977-39260478	MCF-7	breast:	n/a	chr13:39260205-39260223
34	RAD21	chr13:39259958-39260460	ECC-1	luminal epithelium:	n/a	n/a
35	GATA3	chr13:39260081-39260627	T-47D	breast:	n/a	n/a
36	MAX	chr13:39260091-39261370	MCF-7	breast:	n/a	chr13:39260787-39260796
37	JUND	chr13:39260083-39260750	T-47D	breast:	n/a	chr13:39260574-39260583 chr13:39260520-39260532
38	CTCF	chr13:39260000-39260150	HFF-Myc	foreskin:	n/a	n/a
39	SETDB1	chr13:39260078-39261495	U2OS	brain:	n/a	n/a
40	CTCF	chr13:39260100-39260250	HAc	cerebellar:	n/a	chr13:39260205-39260223
41	SMC3	chr13:39260105-39260323	Hela-S3	cervix:	n/a	chr13:39260207-39260221
42	FOXM1	chr13:39260104-39260750	MCF-7	breast:	n/a	n/a
43	RAD21	chr13:39260070-39260456	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr13:39260118-39260339	T-47D	breast:	n/a	chr13:39260205-39260223
45	CTCF	chr13:39260100-39260250	BJ	skin:	n/a	chr13:39260205-39260223
46	CTCF	chr13:39260120-39260270	SK-N-SH_RA	brain:	n/a	chr13:39260205-39260223
47	SRF	chr13:39260121-39260871	MCF-7	breast:	n/a	n/a
48	CTCF	chr13:39260120-39260270	HPAF	blood vessel:	n/a	chr13:39260205-39260223
49	CTCF	chr13:39260120-39260270	RPTEC	kidney:	n/a	chr13:39260205-39260223
50	JUND	chr13:39260064-39260688	T-47D	breast:	n/a	chr13:39260574-39260583 chr13:39260520-39260532

No.	Distal block	Cell Line	Cell type
1	chr13:39256386..39258055-chr13:39258985..39261054,2	MCF-7	breast:
2	chr13:39251483..39253844-chr13:39259100..39260979,2	MCF-7	breast:
3	chr13:39259930..39261837-chr13:39400225..39402249,2	MCF-7	breast:
4	chr13:39259792..39260558-chr13:39309282..39310133,2	MCF-7	breast:
5	chr13:39259605..39260560-chr13:39446509..39447532,4	MCF-7	breast:
6	chr13:39259853..39260679-chr13:39446387..39447489,3	MCF-7	breast:
7	chr13:39258919..39260831-chr13:39305195..39307479,2	MCF-7	breast:
8	chr13:39259609..39260600-chr13:39337776..39338558,4	MCF-7	breast:
9	chr13:39259553..39261802-chr13:39611603..39613271,2	MCF-7	breast:
10	chr13:39244482..39246478-chr13:39258303..39260583,2	MCF-7	breast:
11	chr13:39259811..39260806-chr13:39337692..39338863,8	MCF-7	breast:
12	chr13:39255037..39256959-chr13:39258816..39261083,2	MCF-7	breast:

Variant related genes	Relation type
FREM2	TF binding region
ENSG00000225350	Chromatin interaction
ENSG00000120685	Chromatin interaction
ENSG00000188811	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11147723	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11147724	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11147725	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244358	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2053848	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2122208	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2122212	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2197879	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442335	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442339	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442340	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442341	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442343	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442344	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2442379	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2496418	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496419	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496420	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496425	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2496433	0.80[ASN][1000 genomes]
rs35378642	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4329795	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55860060	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55880170	0.80[ASN][1000 genomes]
rs55922882	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563629	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7331440	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7991701	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs895895	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs930659	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs930660	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9566354	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9576589	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576590	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576591	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576592	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576595	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9634754	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9788341	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39255200-39260200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:39255800-39260200	Weak transcription	Adipose Nuclei	Adipose
3	chr13:39258000-39260400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:39259000-39260200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr13:39259000-39260200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr13:39259600-39260200	Enhancers	Brain Germinal Matrix	brain
7	chr13:39259600-39260200	Enhancers	HMEC	breast
8	chr13:39259600-39260600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:39259600-39260600	Enhancers	Placenta	Placenta
10	chr13:39259600-39261800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr13:39259600-39262000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr13:39259800-39260200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr13:39259800-39260200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr13:39259800-39260200	Enhancers	Brain Hippocampus Middle	brain
15	chr13:39259800-39260200	Bivalent Enhancer	Fetal Lung	lung
16	chr13:39259800-39260800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr13:39259800-39261400	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr13:39259800-39262000	Active TSS	Fetal Kidney	kidney
19	chr13:39260000-39260200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr13:39260000-39260200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:39260000-39260200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr13:39260000-39260200	Enhancers	Liver	Liver
23	chr13:39260000-39260200	Flanking Active TSS	Fetal Heart	heart
24	chr13:39260000-39260200	Flanking Active TSS	Fetal Intestine Small	intestine
25	chr13:39260000-39260200	Enhancers	Stomach Smooth Muscle	stomach
26	chr13:39260000-39260400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr13:39260000-39261000	Active TSS	Fetal Intestine Large	intestine
28	chr13:39260000-39261600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr13:39260000-39261600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:39260000-39261800	Active TSS	H1 Cell Line	embryonic stem cell
31	chr13:39260000-39261800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:39260000-39261800	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr13:39260000-39261800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr13:39260000-39261800	Active TSS	Aorta	Aorta
35	chr13:39260000-39262000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr13:39260000-39262000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:39260000-39262000	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr13:39260000-39262200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr13:39260000-39262200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr13:39260000-39262200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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