Variant report

Variant	rs12891975
Chromosome Location	chr14:71789862-71789863
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	chr14:71789344-71789891	GM12878	blood:	n/a	chr14:71789547-71789566
2	TBP	chr14:71789399-71790253	GM12878	blood:	n/a	n/a
3	POLR2A	chr14:71789334-71789915	GM12878	blood:	n/a	n/a
4	MXI1	chr14:71786032-71789994	SK-N-SH	brain:	n/a	chr14:71786940-71786955 chr14:71786938-71786953
5	STAT3	chr14:71789365-71789952	GM12878	blood:	n/a	n/a
6	TCF7L2	chr14:71789571-71789909	Hela-S3	cervix:	n/a	chr14:71789819-71789835 chr14:71789823-71789832
7	CTCF	chr14:71789366-71789978	K562	blood:	n/a	chr14:71789548-71789569
8	STAT1	chr14:71789536-71789921	GM12878	blood:	n/a	n/a
9	SMC3	chr14:71787824-71789963	GM12878	blood:	n/a	n/a
10	POLR2A	chr14:71789338-71789923	GM12878	blood:	n/a	n/a
11	POLR2A	chr14:71786672-71789921	IMR90	lung:	n/a	n/a
12	CTCF	chr14:71788914-71790060	SK-N-SH	brain:	n/a	chr14:71789548-71789569
13	RAD21	chr14:71786162-71790206	SK-N-SH	brain:	n/a	chr14:71789547-71789566 chr14:71787953-71787963 chr14:71787922-71787932 chr14:71787005-71787018 chr14:71787277-71787290 chr14:71787747-71787761
14	RCOR1	chr14:71789470-71790014	GM12878	blood:	n/a	n/a
15	SMC3	chr14:71789266-71790249	SK-N-SH	brain:	n/a	n/a
16	RAD21	chr14:71789346-71789942	Hela-S3	cervix:	n/a	chr14:71789547-71789566
17	CTCF	chr14:71789335-71790002	GM12878	blood:	n/a	chr14:71789548-71789569
18	TBL1XR1	chr14:71789400-71789947	GM12878	blood:	n/a	n/a
19	RAD21	chr14:71789370-71789958	GM12878	blood:	n/a	chr14:71789547-71789566
20	RFX5	chr14:71788311-71790000	Hela-S3	cervix:	n/a	n/a
21	MXI1	chr14:71789383-71790144	GM12878	blood:	n/a	n/a
22	BCLAF1	chr14:71789308-71789995	GM12878	blood:	n/a	n/a
23	RAD21	chr14:71789207-71789900	MCF-7	breast:	n/a	chr14:71789547-71789566
24	RUNX3	chr14:71789308-71789971	GM12878	blood:	n/a	n/a
25	CTCF	chr14:71789840-71789868	GM10248	blood:	n/a	n/a
26	CTCF	chr14:71789820-71789970	GM12864	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:71787272..71789927-chr14:72149469..72152199,2	MCF-7	breast:
2	chr14:71632877..71633633-chr14:71789090..71789926,3	MCF-7	breast:
3	chr14:71789768..71791635-chr14:71800055..71801739,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259146	TF binding region
ENSG00000197555	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs11620632	0.80[ASN][1000 genomes]
rs11627918	0.80[ASN][1000 genomes]
rs11845249	0.80[ASN][1000 genomes]
rs11849508	0.80[ASN][1000 genomes]
rs12127	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12878989	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12879243	0.85[EUR][1000 genomes]
rs12880291	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12880611	0.86[EUR][1000 genomes]
rs12881643	0.89[EUR][1000 genomes]
rs12881957	0.89[EUR][1000 genomes]
rs12884929	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887261	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12889866	0.86[EUR][1000 genomes]
rs12894016	0.85[EUR][1000 genomes]
rs12894478	0.89[EUR][1000 genomes]
rs12896900	0.85[EUR][1000 genomes]
rs12896986	0.86[EUR][1000 genomes]
rs14030	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17178045	0.86[EUR][1000 genomes]
rs17178206	0.86[EUR][1000 genomes]
rs17178234	0.86[EUR][1000 genomes]
rs17178387	0.84[EUR][1000 genomes]
rs17767386	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17767392	0.87[EUR][1000 genomes]
rs17767398	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17767410	0.87[EUR][1000 genomes]
rs17767446	0.90[EUR][1000 genomes]
rs17767499	0.89[EUR][1000 genomes]
rs17767523	0.86[EUR][1000 genomes]
rs17767553	0.86[EUR][1000 genomes]
rs1990241	0.87[EUR][1000 genomes]
rs2108049	0.86[EUR][1000 genomes]
rs2108707	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2109276	0.86[EUR][1000 genomes]
rs2286409	0.81[AFR][1000 genomes]
rs2877729	0.85[EUR][1000 genomes]
rs33994051	0.86[EUR][1000 genomes]
rs34011442	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34057981	0.85[EUR][1000 genomes]
rs34061264	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34176710	0.85[EUR][1000 genomes]
rs34281405	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34281934	0.87[EUR][1000 genomes]
rs34320622	0.86[EUR][1000 genomes]
rs34347034	0.85[EUR][1000 genomes]
rs34388001	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34454371	0.85[EUR][1000 genomes]
rs34469007	0.86[EUR][1000 genomes]
rs34524083	0.90[EUR][1000 genomes]
rs34528013	0.87[EUR][1000 genomes]
rs34528131	0.90[EUR][1000 genomes]
rs34533948	0.90[EUR][1000 genomes]
rs34649709	0.89[EUR][1000 genomes]
rs34674149	0.87[EUR][1000 genomes]
rs34725136	0.90[EUR][1000 genomes]
rs34746156	0.89[EUR][1000 genomes]
rs34748537	0.90[EUR][1000 genomes]
rs34767050	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34873919	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34911660	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34957192	0.85[EUR][1000 genomes]
rs34991781	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34993988	0.89[EUR][1000 genomes]
rs35051046	0.89[EUR][1000 genomes]
rs35054229	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35094946	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35122644	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35151594	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35260692	0.90[EUR][1000 genomes]
rs35468256	0.89[EUR][1000 genomes]
rs35589413	0.84[EUR][1000 genomes]
rs35609708	0.84[EUR][1000 genomes]
rs35613269	0.86[EUR][1000 genomes]
rs35620527	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35621718	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35625243	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35680546	0.85[EUR][1000 genomes]
rs35692397	0.86[EUR][1000 genomes]
rs35796129	0.90[EUR][1000 genomes]
rs35822724	0.90[EUR][1000 genomes]
rs35831373	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35854505	0.89[EUR][1000 genomes]
rs35866366	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36052007	0.84[EUR][1000 genomes]
rs36057816	0.87[EUR][1000 genomes]
rs36072220	0.80[EUR][1000 genomes]
rs36093218	0.87[EUR][1000 genomes]
rs4453405	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4899394	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4902928	0.84[ASN][1000 genomes]
rs56180634	0.82[EUR][1000 genomes]
rs56363446	0.87[EUR][1000 genomes]
rs56407721	0.89[EUR][1000 genomes]
rs59697713	0.80[ASN][1000 genomes]
rs61989245	0.80[ASN][1000 genomes]
rs61989246	0.80[ASN][1000 genomes]
rs61989247	0.80[ASN][1000 genomes]
rs61989250	0.80[ASN][1000 genomes]
rs61989257	0.80[ASN][1000 genomes]
rs61989367	0.86[EUR][1000 genomes]
rs61989373	0.86[EUR][1000 genomes]
rs61989374	0.86[EUR][1000 genomes]
rs61989377	0.85[EUR][1000 genomes]
rs61989379	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61989382	0.84[EUR][1000 genomes]
rs61989386	0.84[EUR][1000 genomes]
rs61991192	0.84[ASN][1000 genomes]
rs61991199	0.89[EUR][1000 genomes]
rs61991200	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61991201	0.89[EUR][1000 genomes]
rs61991202	0.90[EUR][1000 genomes]
rs61991203	0.87[EUR][1000 genomes]
rs61991204	0.87[EUR][1000 genomes]
rs61991205	0.87[EUR][1000 genomes]
rs61991213	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61991243	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61991246	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61991247	0.90[EUR][1000 genomes]
rs61991248	0.90[EUR][1000 genomes]
rs61991249	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61991250	0.88[EUR][1000 genomes]
rs61991254	0.82[EUR][1000 genomes]
rs61991255	0.86[EUR][1000 genomes]
rs66645707	0.84[EUR][1000 genomes]
rs67489015	0.89[EUR][1000 genomes]
rs68073803	0.90[EUR][1000 genomes]
rs7140354	0.87[EUR][1000 genomes]
rs7142180	0.87[EUR][1000 genomes]
rs7142214	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7145755	0.89[EUR][1000 genomes]
rs7147434	0.91[EUR][1000 genomes]
rs7147668	0.90[EUR][1000 genomes]
rs7152842	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7156460	0.90[EUR][1000 genomes]
rs7160460	0.80[ASN][1000 genomes]
rs722633	0.86[EUR][1000 genomes]
rs723966	0.87[EUR][1000 genomes]
rs725673	0.86[EUR][1000 genomes]
rs72726701	0.80[ASN][1000 genomes]
rs72726702	0.82[ASN][1000 genomes]
rs72728403	0.84[ASN][1000 genomes]
rs72728427	0.90[EUR][1000 genomes]
rs8007068	0.90[EUR][1000 genomes]
rs8013161	0.82[EUR][1000 genomes]
rs8015644	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8019721	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	nsv832827	chr14:71676178-71833519	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv1831401	chr14:71786411-71845264	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71786200-71790000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr14:71786400-71790000	Active TSS	Brain Hippocampus Middle	brain
3	chr14:71786400-71790000	Active TSS	HSMM	muscle
4	chr14:71786400-71790000	Active TSS	HSMMtube	muscle
5	chr14:71786400-71790200	Active TSS	Stomach Mucosa	stomach
6	chr14:71786600-71790000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr14:71786600-71790000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr14:71786800-71790000	Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr14:71786800-71790200	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr14:71787000-71791400	Active TSS	GM12878-XiMat	blood
11	chr14:71788200-71790000	Flanking Active TSS	Dnd41	blood
12	chr14:71788200-71790600	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr14:71788200-71790600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr14:71788400-71790000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr14:71788400-71790600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr14:71788600-71790000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr14:71788600-71791600	Weak transcription	Small Intestine	intestine
18	chr14:71788600-71792800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr14:71788600-71794600	Weak transcription	Gastric	stomach
20	chr14:71788600-71811200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr14:71788600-71817000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr14:71788800-71791600	Weak transcription	Pancreas	Pancrea
23	chr14:71788800-71791600	Weak transcription	Spleen	Spleen
24	chr14:71788800-71793400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr14:71789000-71790000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr14:71789000-71790000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr14:71789000-71790000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr14:71789000-71790000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:71789000-71790000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr14:71789000-71790000	Active TSS	NHLF	lung
31	chr14:71789000-71790200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr14:71789000-71790200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr14:71789000-71790200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr14:71789000-71790200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr14:71789000-71790400	Flanking Active TSS	HMEC	breast
36	chr14:71789000-71790600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr14:71789000-71790600	Flanking Active TSS	Osteobl	bone
38	chr14:71789000-71791400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr14:71789000-71791400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr14:71789000-71791400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr14:71789000-71791400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr14:71789000-71791400	Weak transcription	Fetal Thymus	thymus
43	chr14:71789000-71791400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr14:71789000-71791600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr14:71789000-71791600	Weak transcription	Left Ventricle	heart
46	chr14:71789000-71791800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr14:71789000-71791800	Weak transcription	Colonic Mucosa	Colon
48	chr14:71789000-71792600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr14:71789000-71793400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr14:71789000-71793400	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links