Variant report

Variant	rs956910
Chromosome Location	chr12:46759788-46759789
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	RCOR1	chr12:46759716-46760040	HepG2	liver:	n/a	n/a
2	ATF1	chr12:46759743-46759968	K562	blood:	n/a	n/a
3	POLR2A	chr12:46759518-46760169	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr12:46759681-46760072	GM12891	blood:	n/a	n/a
5	POLR2A	chr12:46754898-46760301	U87	brain:	n/a	n/a
6	POLR2A	chr12:46750625-46766899	K562	blood:	n/a	n/a
7	SPI1	chr12:46759675-46759884	GM12891	blood:	n/a	n/a
8	POLR2A	chr12:46758700-46760175	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr12:46756521-46767732	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:46759638-46760128	K562	blood:	n/a	n/a
11	POLR2A	chr12:46757569-46760144	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:46750469-46766708	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:46758728-46760155	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:46758723-46760310	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr12:46750482-46767845	Hela-S3	cervix:	n/a	n/a
16	SPI1	chr12:46759701-46759898	K562	blood:	n/a	n/a
17	POLR2A	chr12:46754517-46767857	HepG2	liver:	n/a	n/a
18	POLR2A	chr12:46759685-46760228	K562	blood:	n/a	n/a
19	POLR2A	chr12:46750751-46768006	HepG2	liver:	n/a	n/a
20	SPI1	chr12:46759699-46759968	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:46758662-46766869	HUVEC	blood vessel:	n/a	n/a
22	CHD1	chr12:46756240-46768821	IMR90	lung:	n/a	chr12:46765445-46765455 chr12:46766470-46766477 chr12:46768496-46768506 chr12:46768499-46768509
23	FOXA1	chr12:46759702-46760071	T-47D	breast:	n/a	n/a
24	JUND	chr12:46758678-46760244	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr12:46759589-46760308	K562	blood:	n/a	n/a
26	POLR2A	chr12:46754387-46768013	PANC-1	pancreas:	n/a	n/a
27	FOXA1	chr12:46759556-46760104	HepG2	liver:	n/a	n/a
28	POLR2A	chr12:46754499-46767455	HUVEC	blood vessel:	n/a	n/a
29	FOXA1	chr12:46759637-46760082	HepG2	liver:	n/a	n/a
30	POLR2A	chr12:46759500-46760307	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:46757607-46767342	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr12:46750487-46766675	A549	lung:	n/a	n/a
33	POLR2A	chr12:46758684-46767978	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr12:46759507-46760414	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr12:46758139-46766914	MCF-7	breast:	n/a	n/a
36	POLR2A	chr12:46759667-46760136	GM12878	blood:	n/a	n/a
37	GATA3	chr12:46758922-46760195	A549	lung:	n/a	chr12:46759305-46759312 chr12:46759305-46759312 chr12:46759298-46759319 chr12:46759305-46759314 chr12:46759305-46759312
38	POLR2A	chr12:46754358-46767861	HepG2	liver:	n/a	n/a
39	MBD4	chr12:46756528-46760338	HepG2	liver:	n/a	n/a
40	POLR2A	chr12:46759684-46760199	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr12:46759502-46760185	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr12:46755082-46767953	HCT-116	colon:	n/a	n/a
43	POLR2A	chr12:46758424-46767361	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr12:46750385-46767599	IMR90	lung:	n/a	n/a
45	POLR2A	chr12:46759416-46760468	K562	blood:	n/a	n/a
46	HEY1	chr12:46750801-46768173	HepG2	liver:	n/a	chr12:46766614-46766629 chr12:46766074-46766089 chr12:46765229-46765244
47	POLR2A	chr12:46759547-46760150	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr12:46758649-46760326	PANC-1	pancreas:	n/a	n/a
49	SPI1	chr12:46759579-46760058	HL-60	blood:	n/a	n/a
50	ZMIZ1	chr12:46759756-46759857	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
2	chr12:46660616..46664726-chr12:46759249..46761419,3	MCF-7	breast:
3	chr12:46661733..46663238-chr12:46759583..46762194,2	K562	blood:
4	chr12:46658898..46664029-chr12:46756711..46760586,4	K562	blood:
5	chr12:46759096..46760660-chr12:46901323..46903298,2	MCF-7	breast:

Variant related genes	Relation type
SLC38A2	TF binding region
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10467213	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1079780	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10880947	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs10880953	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10880959	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10880960	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880961	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10880966	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs11183441	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12302984	0.81[EUR][1000 genomes]
rs12310125	0.87[CEU][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs12311507	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12317787	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12320197	0.85[CEU][hapmap];0.83[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap]
rs12580583	0.82[EUR][1000 genomes]
rs12813763	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap]
rs12814341	0.84[CEU][hapmap]
rs12816358	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12816413	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1471223	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1492892	0.88[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1492894	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1873793	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs2018424	0.81[EUR][1000 genomes]
rs2087834	0.81[EUR][1000 genomes]
rs2169030	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2172398	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs2242355	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs2307061	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2408504	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2408505	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2408506	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2408507	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2408508	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2897968	0.92[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34119192	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35123676	0.81[EUR][1000 genomes]
rs35497251	0.81[EUR][1000 genomes]
rs3782904	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238102	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4438106	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4547171	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4586238	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4768111	0.82[EUR][1000 genomes]
rs4768115	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768116	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768694	0.81[EUR][1000 genomes]
rs4768695	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4768696	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59919892	0.81[EUR][1000 genomes]
rs6582656	0.83[CHD][hapmap]
rs7132228	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7134855	0.82[EUR][1000 genomes]
rs7310869	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7314069	0.82[EUR][1000 genomes]
rs7315493	0.88[CEU][hapmap]
rs7316127	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs7316773	0.88[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs7953659	0.81[EUR][1000 genomes]
rs7958774	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7960147	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7961994	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7967669	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7968173	1.00[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7968283	1.00[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7974529	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976280	0.84[CEU][hapmap];0.90[CHD][hapmap]
rs7976362	0.82[EUR][1000 genomes]
rs7979418	0.88[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7979514	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7980775	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs898242	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9668077	0.84[AMR][1000 genomes]
rs9669051	0.85[EUR][1000 genomes]
rs9669381	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9795971	0.93[AMR][1000 genomes];0.85[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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs956910	SLC24A3	trans	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46737600-46761200	Weak transcription	Gastric	stomach
2	chr12:46744000-46760600	Weak transcription	Spleen	Spleen
3	chr12:46748800-46764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:46750400-46761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:46751600-46760600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:46751600-46761200	Strong transcription	Fetal Brain Female	brain
7	chr12:46752200-46761200	Strong transcription	Placenta	Placenta
8	chr12:46752400-46759800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:46752400-46760400	Strong transcription	Brain Germinal Matrix	brain
10	chr12:46752400-46761400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:46752400-46761600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:46752400-46761600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:46752400-46761800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:46752400-46764200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:46752600-46760600	Strong transcription	Fetal Thymus	thymus
16	chr12:46752600-46761200	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr12:46752600-46761200	Strong transcription	Fetal Muscle Leg	muscle
18	chr12:46752600-46761400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr12:46752600-46761600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:46752600-46762400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:46752600-46763000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:46752600-46763600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:46752600-46764200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:46752800-46760600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:46752800-46761200	Strong transcription	Left Ventricle	heart
26	chr12:46752800-46761600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:46752800-46762000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:46753000-46761000	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:46753000-46762600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:46753200-46760400	Weak transcription	Fetal Stomach	stomach
31	chr12:46753200-46761000	Strong transcription	Fetal Kidney	kidney
32	chr12:46753400-46761200	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr12:46753400-46761800	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr12:46753400-46762400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:46753400-46764200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:46753600-46761200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr12:46753600-46761600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:46753600-46765200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:46754000-46759800	Weak transcription	Pancreas	Pancrea
40	chr12:46754000-46761200	Genic enhancers	Primary T cells from cord blood	blood
41	chr12:46754000-46761200	Weak transcription	Esophagus	oesophagus
42	chr12:46754000-46765800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:46754600-46762600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr12:46754600-46765000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
45	chr12:46754800-46759800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:46754800-46759800	Genic enhancers	Liver	Liver
47	chr12:46754800-46762600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr12:46755400-46766000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:46755800-46759800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:46755800-46760000	Strong transcription	Primary monocytes fromperipheralblood	blood

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