Variant report

Variant	rs3809310
Chromosome Location	chr12:121087072-121087073
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	CHD2	chr12:121086990-121087332	Hela-S3	cervix:	n/a	n/a
2	ZC3H11A	chr12:121087017-121087321	K562	blood:	n/a	n/a
3	CEBPB	chr12:121086972-121087172	K562	blood:	n/a	n/a
4	CTCF	chr12:121087053-121087330	Pancreas_OC	pancreas:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
5	RAD21	chr12:121086703-121087550	HCT-116	colon:	n/a	chr12:121087170-121087183 chr12:121087167-121087186 chr12:121087171-121087181 chr12:121087169-121087181 chr12:121086760-121086770
6	TCF12	chr12:121086609-121087372	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr12:121087004-121087558	GM12892	blood:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
8	CREB1	chr12:121086614-121087393	H1-hESC	embryonic stem cell:	n/a	n/a
9	CREB1	chr12:121086955-121087618	A549	lung:	n/a	n/a
10	BACH1	chr12:121086735-121087449	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr12:121086859-121087373	A549	lung:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
12	RCOR1	chr12:121087000-121087256	K562	blood:	n/a	n/a
13	ZMIZ1	chr12:121087057-121087195	K562	blood:	n/a	n/a
14	POLR2A	chr12:121086948-121087218	K562	blood:	n/a	n/a
15	MAX	chr12:121086856-121087422	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAZ	chr12:121086970-121087305	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr12:121086881-121087425	MCF-7	breast:	n/a	chr12:121087170-121087183 chr12:121087167-121087186 chr12:121087171-121087181 chr12:121087169-121087181
18	MAX	chr12:121086903-121087433	SK-N-SH	brain:	n/a	chr12:121087423-121087433
19	CTCF	chr12:121087060-121087210	GM12869	blood:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
20	CTCF	chr12:121086985-121087588	GM19238	blood:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
21	CTCF	chr12:121087040-121087300	SK-N-SH_RA	brain:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
22	MAX	chr12:121087028-121087248	K562	blood:	n/a	n/a
23	CTCF	chr12:121086928-121087502	MCF-7	breast:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
24	CTCF	chr12:121087055-121087311	GM13977	blood:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
25	RUNX3	chr12:121086923-121087347	GM12878	blood:	n/a	n/a
26	CTCF	chr12:121087008-121087331	GM12891	blood:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
27	ELF1	chr12:121086905-121087472	GM12878	blood:	n/a	n/a
28	CTCF	chr12:121087060-121087210	A549	lung:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
29	RAD21	chr12:121086960-121087337	H1-hESC	embryonic stem cell:	n/a	chr12:121087170-121087183 chr12:121087167-121087186 chr12:121087171-121087181 chr12:121087169-121087181
30	WRNIP1	chr12:121086931-121087341	GM12878	blood:	n/a	n/a
31	CTCF	chr12:121087060-121087210	HCM	heart:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
32	CTCF	chr12:121086991-121087313	GM19239	blood:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
33	GABPA	chr12:121086951-121087363	H1-hESC	embryonic stem cell:	n/a	n/a
34	E2F6	chr12:121086998-121087852	H1-hESC	embryonic stem cell:	n/a	chr12:121087058-121087068
35	CTCF	chr12:121087060-121087210	AG04450	lung:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
36	CTCF	chr12:121086690-121087486	HCT-116	colon:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
37	ELF1	chr12:121087039-121087292	HepG2	liver:	n/a	n/a
38	CTCF	chr12:121087029-121087321	K562	blood:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
39	CHD2	chr12:121086741-121087376	GM12878	blood:	n/a	n/a
40	RAD21	chr12:121086892-121087312	A549	lung:	n/a	chr12:121087170-121087183 chr12:121087167-121087186 chr12:121087171-121087181 chr12:121087169-121087181
41	FOXM1	chr12:121086896-121087448	GM12878	blood:	n/a	n/a
42	REST	chr12:121087009-121087312	A549	lung:	n/a	n/a
43	ZNF143	chr12:121087021-121087272	Hela-S3	cervix:	n/a	chr12:121087021-121087031
44	CTCF	chr12:121086989-121087546	GM19240	blood:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
45	PAX5	chr12:121086482-121087293	GM12878	blood:	n/a	chr12:121086802-121086819
46	CTCF	chr12:121087060-121087304	GM10248	blood:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184
47	STAT1	chr12:121086896-121087330	GM12878	blood:	n/a	n/a
48	RAD21	chr12:121086863-121087479	H1-hESC	embryonic stem cell:	n/a	chr12:121087170-121087183 chr12:121087167-121087186 chr12:121087171-121087181 chr12:121087169-121087181
49	ZNF143	chr12:121086966-121087390	GM12878	blood:	n/a	chr12:121087021-121087031
50	CTCF	chr12:121087024-121087331	GM12878	blood:	n/a	chr12:121087164-121087185 chr12:121087169-121087187 chr12:121087170-121087186 chr12:121087171-121087184 chr12:121087175-121087184

No.	Distal block	Cell Line	Cell type
1	chr12:121085752..121087777-chr12:121138546..121140930,2	MCF-7	breast:
2	chr12:120882880..120885596-chr12:121086494..121088113,2	K562	blood:
3	chr12:121020090..121020910-chr12:121086635..121087738,3	MCF-7	breast:
4	chr12:121021209..121021867-chr12:121087027..121087660,3	MCF-7	breast:
5	chr12:121074234..121078810-chr12:121086912..121091656,5	K562	blood:
6	chr12:121084859..121087400-chr12:121088955..121093657,4	MCF-7	breast:
7	chr12:121085923..121088804-chr12:121121977..121126483,5	MCF-7	breast:
8	chr12:121086713..121087372-chr12:121107159..121108129,2	MCF-7	breast:
9	chr12:120762972..120763850-chr12:121086347..121087643,3	K562	blood:
10	chr12:121085668..121087390-chr12:121148054..121149834,2	MCF-7	breast:
11	chr12:121085946..121088715-chr12:121122622..121126229,3	K562	blood:
12	chr12:121079111..121082636-chr12:121084242..121087390,3	K562	blood:

Variant related genes	Relation type
CABP1	TF binding region
ENSG00000256008	Chromatin interaction
ENSG00000110917	Chromatin interaction
ENSG00000170855	Chromatin interaction
ENSG00000157782	Chromatin interaction
ENSG00000257218	Chromatin interaction
ENSG00000175970	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10431372	0.86[EUR][1000 genomes]
rs10431383	0.86[EUR][1000 genomes]
rs10774564	0.93[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs10774565	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs10849774	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10849775	0.92[ASN][1000 genomes]
rs10849780	0.86[EUR][1000 genomes]
rs10849781	1.00[ASW][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11065183	0.88[ASN][1000 genomes]
rs11065184	0.93[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065188	0.93[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11065189	0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11065191	0.83[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065192	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065193	0.82[ASN][1000 genomes]
rs11065194	0.87[CHB][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065195	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11065196	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11065197	0.87[CHB][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065198	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065199	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065204	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065205	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11065214	0.86[EUR][1000 genomes]
rs11065215	0.86[EUR][1000 genomes]
rs11065217	0.86[EUR][1000 genomes]
rs11065220	0.86[EUR][1000 genomes]
rs11065221	0.86[EUR][1000 genomes]
rs11065224	0.86[EUR][1000 genomes]
rs11065229	0.86[EUR][1000 genomes]
rs11065234	0.86[EUR][1000 genomes]
rs11065235	1.00[ASW][hapmap];0.86[EUR][1000 genomes]
rs11065244	0.86[EUR][1000 genomes]
rs12228118	0.86[EUR][1000 genomes]
rs12228187	0.93[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12229164	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12229181	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12231499	0.86[EUR][1000 genomes]
rs12310160	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs17848090	0.86[EUR][1000 genomes]
rs2071266	0.86[EUR][1000 genomes]
rs2229534	1.00[ASW][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2239687	0.86[EUR][1000 genomes]
rs2239757	0.86[EUR][1000 genomes]
rs2239759	0.86[EUR][1000 genomes]
rs3751166	0.86[EUR][1000 genomes]
rs3809311	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7302002	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7956304	0.81[CHD][hapmap]
rs7973568	1.00[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1045923	chr12:121082203-121146219	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121086600-121087200	Enhancers	Primary B cells from cord blood	blood
2	chr12:121086600-121087400	Bivalent Enhancer	Dnd41	blood
3	chr12:121086600-121087800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
4	chr12:121086600-121088200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:121086800-121087200	Active TSS	H1 Cell Line	embryonic stem cell
6	chr12:121086800-121087200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:121086800-121087200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:121086800-121087200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr12:121086800-121087200	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr12:121086800-121087200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:121086800-121087200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:121086800-121087200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:121086800-121087200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:121086800-121087200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:121086800-121087200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:121086800-121087200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:121086800-121087200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:121086800-121087200	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
19	chr12:121086800-121087200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr12:121086800-121087200	Active TSS	Primary hematopoietic stem cells	blood
21	chr12:121086800-121087200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
22	chr12:121086800-121087200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:121086800-121087200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:121086800-121087200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
25	chr12:121086800-121087200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:121086800-121087200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:121086800-121087200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr12:121086800-121087200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr12:121086800-121087200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr12:121086800-121087200	Flanking Active TSS	Fetal Intestine Small	intestine
31	chr12:121086800-121087200	Flanking Active TSS	Fetal Stomach	stomach
32	chr12:121086800-121087200	Flanking Active TSS	Ovary	ovary
33	chr12:121086800-121087200	Active TSS	Rectal Smooth Muscle	rectum
34	chr12:121086800-121087200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr12:121086800-121087200	Flanking Active TSS	HMEC	breast
36	chr12:121086800-121087200	Active TSS	HSMM	muscle
37	chr12:121086800-121087200	Bivalent/Poised TSS	HSMMtube	muscle
38	chr12:121086800-121087200	Active TSS	K562	blood
39	chr12:121086800-121087200	Flanking Active TSS	NH-A	brain
40	chr12:121086800-121087200	Flanking Active TSS	NHEK	skin
41	chr12:121086800-121087200	Active TSS	NHLF	lung
42	chr12:121086800-121087400	Active TSS	H9 Cell Line	embryonic stem cell
43	chr12:121086800-121087400	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr12:121086800-121087400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:121086800-121087400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
46	chr12:121086800-121087400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:121086800-121087400	Active TSS	Aorta	Aorta
48	chr12:121086800-121087400	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr12:121086800-121087400	Active TSS	Colon Smooth Muscle	Colon
50	chr12:121086800-121087400	Bivalent Enhancer	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links