Variant report

Variant	rs7304797
Chromosome Location	chr12:40218421-40218422
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	RAD21	chr12:40218313-40219099	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr12:40218341-40218751	HepG2	liver:	n/a	n/a
3	STAT3	chr12:40218336-40219073	MCF10A-Er-Src	breast:	n/a	chr12:40218804-40218815
4	RAD21	chr12:40218410-40218660	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr12:40218373-40218723	GM12878	blood:	n/a	n/a
6	FOS	chr12:40218372-40218572	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr12:40218369-40218576	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr12:40218351-40219057	MCF10A-Er-Src	breast:	n/a	chr12:40218804-40218815
9	RAD21	chr12:40218344-40218790	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr12:40218421-40218614	A549	lung:	n/a	n/a
11	FOS	chr12:40218380-40218527	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr12:40218325-40219007	Hela-S3	cervix:	n/a	chr12:40218888-40218899
13	RAD21	chr12:40218404-40218640	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:40218260-40218647	MCF10A-Er-Src	breast:	n/a	n/a
15	RAD21	chr12:40218403-40218661	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr12:40218421-40218811	SK-N-SH	brain:	n/a	n/a
17	STAT3	chr12:40218335-40219074	MCF10A-Er-Src	breast:	n/a	chr12:40218804-40218815
18	RAD21	chr12:40218377-40218832	A549	lung:	n/a	n/a
19	STAT3	chr12:40218306-40219157	MCF10A-Er-Src	breast:	n/a	chr12:40218804-40218815

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40218165..40218758-chr12:40352165..40352674,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199571	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10747886	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747932	0.84[ASN][1000 genomes]
rs10784079	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784118	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10784208	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784223	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784228	0.81[ASN][1000 genomes]
rs10784234	0.82[CEU][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877533	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11173822	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12813110	0.87[ASN][1000 genomes]
rs4293188	0.81[CEU][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4310675	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4350423	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4357761	0.94[ASN][1000 genomes]
rs4370998	0.84[ASN][1000 genomes]
rs4382970	0.84[ASN][1000 genomes]
rs4388962	0.84[ASN][1000 genomes]
rs4423249	0.81[EUR][1000 genomes]
rs4429129	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4433640	0.81[CEU][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4473001	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4473002	0.88[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4531537	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4539398	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4579982	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4598727	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604958	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638370	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4638371	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768188	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768189	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6581365	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6581378	0.92[CEU][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581403	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6581405	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7133478	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7134335	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7135701	0.81[CEU][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7294916	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295029	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7295344	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7299208	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7306234	0.84[CEU][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7308155	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315452	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7358574	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958983	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959259	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7960098	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7961625	0.82[CEU][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7962260	0.88[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963511	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963645	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966294	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967956	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7968509	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9668722	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1052012	chr12:40180398-40237782	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1040628	chr12:40180398-40244001	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv899025	chr12:40191778-40321846	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1049214	chr12:40197549-40326495	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40193800-40255800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40194600-40232600	Weak transcription	Right Ventricle	heart
3	chr12:40199200-40265400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:40206200-40221200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:40209200-40268800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:40209400-40249800	Weak transcription	Aorta	Aorta
7	chr12:40210000-40225400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:40213000-40248200	Weak transcription	Fetal Intestine Large	intestine
9	chr12:40214000-40223600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:40214200-40223600	Weak transcription	Left Ventricle	heart
11	chr12:40216000-40246600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:40216600-40223400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:40218000-40219400	Enhancers	Liver	Liver
14	chr12:40218200-40219400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:40218200-40225000	Weak transcription	Small Intestine	intestine
16	chr12:40218400-40219000	Enhancers	Hela-S3	cervix
17	chr12:40218400-40219600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:40218400-40224400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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