Variant report

Variant	rs2694008
Chromosome Location	chr12:56132824-56132825
allele	A/G
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	SMC3	chr12:56132570-56133019	K562	blood:	n/a	chr12:56132752-56132766
2	CTCF	chr12:56132628-56132848	GM10248	blood:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
3	RAD21	chr12:56132374-56132998	SK-N-SH_RA	brain:	n/a	chr12:56132751-56132770
4	RCOR1	chr12:56132131-56132918	Hela-S3	cervix:	n/a	n/a
5	RAD21	chr12:56132206-56132980	H1-hESC	embryonic stem cell:	n/a	chr12:56132751-56132770
6	PML	chr12:56131608-56133004	GM12878	blood:	n/a	n/a
7	CTCF	chr12:56132680-56132830	BE2_C	brain:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
8	CTCF	chr12:56132680-56132830	GM12866	blood:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
9	MAFF	chr12:56132492-56132889	HepG2	liver:	n/a	n/a
10	CTCF	chr12:56132680-56132830	AoAF	blood vessel:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
11	CTCF	chr12:56132535-56132868	A549	lung:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
12	MXI1	chr12:56131378-56133222	IMR90	lung:	n/a	chr12:56132303-56132318 chr12:56132305-56132320 chr12:56132351-56132366
13	RFX5	chr12:56131887-56132834	GM12878	blood:	n/a	chr12:56132303-56132320 chr12:56132304-56132319 chr12:56132348-56132362 chr12:56132350-56132365 chr12:56132304-56132319 chr12:56132347-56132362 chr12:56132304-56132319 chr12:56132351-56132360
14	CTCF	chr12:56132720-56132870	GM12864	blood:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
15	CTCF	chr12:56132680-56132830	HPF	lung:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
16	MAZ	chr12:56131688-56132903	GM12878	blood:	n/a	chr12:56132372-56132382
17	CTCF	chr12:56132700-56132850	SK-N-SH_RA	brain:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
18	CTCF	chr12:56132680-56132830	NHEK	skin:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
19	RCOR1	chr12:56132158-56132881	K562	blood:	n/a	n/a
20	CTCF	chr12:56132700-56132850	HMF	breast:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
21	NR2F2	chr12:56131944-56132844	K562	blood:	n/a	n/a
22	RAD21	chr12:56130703-56133189	SK-N-SH	brain:	n/a	chr12:56132751-56132770 chr12:56131745-56131757 chr12:56131304-56131316
23	SMC3	chr12:56131673-56133198	SK-N-SH	brain:	n/a	chr12:56132752-56132766 chr12:56132455-56132462
24	CTCF	chr12:56132222-56132969	GM12878	blood:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
25	CTCF	chr12:56132680-56132830	HCFaa	heart:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
26	CTCF	chr12:56132200-56132982	MCF-7	breast:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
27	SPI1	chr12:56132550-56132901	GM12878	blood:	n/a	chr12:56132713-56132722
28	CTCF	chr12:56132680-56132830	AG10803	skin:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
29	BRCA1	chr12:56132211-56132921	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr12:56132680-56132830	GM12870	blood:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
31	CTCF	chr12:56132563-56132918	SK-N-SH_RA	brain:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
32	CTCF	chr12:56132740-56132890	HEK293	kidney:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
33	MAFK	chr12:56132282-56132867	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr12:56132680-56132830	GM06990	blood:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
35	CTCF	chr12:56132497-56132951	HepG2	liver:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
36	ZNF143	chr12:56131908-56132887	H1-hESC	embryonic stem cell:	n/a	chr12:56132091-56132109
37	CTCF	chr12:56132617-56132876	Kidney_OC	kidney:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
38	MAFK	chr12:56132053-56132874	IMR90	lung:	n/a	n/a
39	CTCF	chr12:56132613-56132973	H1-hESC	embryonic stem cell:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
40	ZNF143	chr12:56132035-56132903	Hela-S3	cervix:	n/a	chr12:56132091-56132109
41	CTCF	chr12:56132680-56132830	HCM	heart:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
42	CTCF	chr12:56132518-56132939	IMR90	lung:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
43	MAFF	chr12:56132498-56132902	K562	blood:	n/a	n/a
44	ZKSCAN1	chr12:56132120-56132875	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr12:56132680-56132830	RPTEC	kidney:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
46	CTCF	chr12:56132680-56132830	GM12875	blood:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
47	SIN3AK20	chr12:56131886-56132847	SK-N-SH	brain:	n/a	n/a
48	RAD21	chr12:56132618-56132911	K562	blood:	n/a	chr12:56132751-56132770
49	CTCF	chr12:56132221-56133087	HCT-116	colon:	n/a	chr12:56132752-56132773 chr12:56132750-56132768
50	ZNF143	chr12:56131939-56132922	GM12878	blood:	n/a	chr12:56132091-56132109

No.	Distal block	Cell Line	Cell type
1	chr12:56131925..56134582-chr12:56510432..56511934,2	K562	blood:
2	chr12:56130509..56134677-chr12:56319153..56322835,6	MCF-7	breast:
3	chr12:56132404..56134196-chr12:56190050..56191592,2	MCF-7	breast:
4	chr12:56132187..56133052-chr12:56423108..56423612,2	MCF-7	breast:
5	chr12:56131366..56133747-chr12:56432632..56435833,3	MCF-7	breast:
6	chr12:56132662..56133230-chr12:56423214..56423718,2	K562	blood:
7	chr12:56132288..56132866-chr12:56434437..56435937,6	K562	blood:
8	chr12:56132399..56133496-chr12:56190540..56191625,4	K562	blood:
9	chr12:56132266..56133131-chr12:56423132..56423720,2	MCF-7	breast:
10	chr12:56132426..56134406-chr12:56222094..56224947,2	MCF-7	breast:
11	chr12:56132312..56134290-chr12:56323764..56326153,3	K562	blood:
12	chr12:56131444..56134724-chr12:56433965..56437201,5	K562	blood:
13	chr12:56130516..56133996-chr12:56433769..56437389,4	MCF-7	breast:
14	chr12:56131182..56132830-chr12:56498013..56500041,2	K562	blood:
15	chr12:56129313..56132874-chr12:56186006..56190990,5	MCF-7	breast:
16	chr12:56132326..56134281-chr12:56145897..56148451,2	K562	blood:
17	chr12:56132645..56133216-chr12:56190707..56191479,2	MCF-7	breast:
18	chr12:56132452..56134425-chr12:56331378..56333977,2	MCF-7	breast:
19	chr12:56132244..56134495-chr12:56518437..56521367,2	MCF-7	breast:
20	chr12:56131235..56133637-chr12:56213720..56215298,2	MCF-7	breast:
21	chr12:56131252..56134582-chr12:56510432..56513329,3	K562	blood:
22	chr12:56132258..56134137-chr12:56430379..56432312,2	MCF-7	breast:
23	chr12:56130904..56133649-chr12:56685067..56686704,2	MCF-7	breast:
24	chr12:56131239..56134879-chr12:56318262..56322483,4	MCF-7	breast:
25	chr12:56132112..56134190-chr12:56615227..56617846,2	K562	blood:
26	chr12:56131540..56134200-chr12:56203491..56206395,2	MCF-7	breast:
27	chr12:56132724..56138260-chr12:56359199..56362083,4	MCF-7	breast:
28	chr12:56132414..56133164-chr12:56190873..56191522,3	MCF-7	breast:
29	chr12:56131361..56133175-chr12:56223077..56224908,2	MCF-7	breast:
30	chr12:56130927..56134179-chr12:56510145..56513079,3	MCF-7	breast:
31	chr12:56132715..56134243-chr12:56134922..56137759,2	MCF-7	breast:
32	chr12:56128998..56134444-chr12:56209748..56213922,6	MCF-7	breast:
33	chr12:56131563..56134235-chr12:56194680..56196236,2	K562	blood:
34	chr12:56131110..56132920-chr12:56139527..56141888,2	K562	blood:
35	chr12:56130710..56134380-chr12:56135389..56139193,10	MCF-7	breast:

Variant related genes	Relation type
GDF11	TF binding region
ENSG00000257449	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000258554	Chromatin interaction
ENSG00000170515	Chromatin interaction
ENSG00000197728	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1466512	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1681085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1725358	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1871999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2449476	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2462938	1.00[AMR][1000 genomes]
rs2694015	1.00[AMR][1000 genomes]
rs2887997	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4759012	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4759202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55884432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6581083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7294345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7305623	1.00[MEX][hapmap]
rs7310325	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs772250	1.00[AMR][1000 genomes]
rs772251	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs772252	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs772253	1.00[AMR][1000 genomes]
rs772256	1.00[AMR][1000 genomes]
rs772257	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs772259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772260	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772261	1.00[AMR][1000 genomes]
rs7956337	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7963379	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs812230	1.00[AFR][1000 genomes];1.00[AMR][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	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56127200-56136000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:56131800-56137200	Weak transcription	Gastric	stomach
3	chr12:56132000-56133000	Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr12:56132000-56133000	Active TSS	Fetal Kidney	kidney
5	chr12:56132000-56136000	Weak transcription	Small Intestine	intestine
6	chr12:56132200-56133000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:56132200-56133000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:56132200-56133000	Active TSS	Thymus	Thymus
9	chr12:56132200-56133000	Active TSS	GM12878-XiMat	blood
10	chr12:56132200-56135800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:56132400-56133000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:56132600-56133000	Active TSS	Stomach Smooth Muscle	stomach
13	chr12:56132600-56135600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:56132600-56135800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:56132600-56136000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:56132600-56136400	Weak transcription	Lung	lung
17	chr12:56132800-56133000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:56132800-56133000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:56132800-56133000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:56132800-56133000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr12:56132800-56133000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr12:56132800-56133000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr12:56132800-56133000	Enhancers	Primary B cells from cord blood	blood
24	chr12:56132800-56133000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr12:56132800-56133000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:56132800-56133000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:56132800-56133000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr12:56132800-56133000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr12:56132800-56133000	Enhancers	Brain Angular Gyrus	brain
30	chr12:56132800-56133000	Enhancers	Brain Anterior Caudate	brain
31	chr12:56132800-56133000	Enhancers	Brain Cingulate Gyrus	brain
32	chr12:56132800-56133000	Enhancers	Brain Germinal Matrix	brain
33	chr12:56132800-56133000	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr12:56132800-56133000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:56132800-56133000	Enhancers	Fetal Brain Female	brain
36	chr12:56132800-56133000	Enhancers	Fetal Intestine Large	intestine
37	chr12:56132800-56133000	Flanking Active TSS	A549	lung
38	chr12:56132800-56133000	Enhancers	HepG2	liver
39	chr12:56132800-56133000	Enhancers	NHEK	skin
40	chr12:56132800-56133200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr12:56132800-56133200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr12:56132800-56133200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:56132800-56133200	Enhancers	Duodenum Mucosa	Duodenum
44	chr12:56132800-56133200	Enhancers	Fetal Heart	heart
45	chr12:56132800-56133200	Enhancers	Dnd41	blood
46	chr12:56132800-56133200	Enhancers	Hela-S3	cervix
47	chr12:56132800-56133800	Enhancers	K562	blood
48	chr12:56132800-56134800	Weak transcription	Fetal Lung	lung
49	chr12:56132800-56135400	Weak transcription	Fetal Brain Male	brain
50	chr12:56132800-56135400	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links