Variant report

Variant	rs4768866
Chromosome Location	chr12:51156580-51156581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:51155897-51159173	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:51153937-51156625	K562	blood:	n/a	n/a
3	TBL1XR1	chr12:51155937-51156632	K562	blood:	n/a	n/a
4	POLR2A	chr12:51155915-51156605	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr12:51156014-51156789	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr12:51154842-51156666	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr12:51154950-51159706	MCF10A-Er-Src	breast:	n/a	n/a
8	JUN	chr12:51155961-51159957	K562	blood:	n/a	chr12:51156279-51156291 chr12:51157952-51157961

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51154627..51156805-chr12:51157397..51159001,2	K562	blood:
2	chr12:51156114..51160622-chr12:51418657..51421869,11	K562	blood:
3	chr12:51135835..51138035-chr12:51156285..51158061,2	MCF-7	breast:
4	chr12:51154877..51158479-chr12:51475248..51478841,3	K562	blood:
5	chr12:51155914..51160622-chr12:51417270..51421869,9	K562	blood:
6	chr12:51155753..51160968-chr12:51475872..51478809,5	MCF-7	breast:
7	chr12:51155985..51158147-chr12:51315840..51318391,2	MCF-7	breast:
8	chr12:51156231..51158960-chr12:51317356..51321250,3	K562	blood:
9	chr12:51156096..51157796-chr12:51717451..51720427,2	MCF-7	breast:
10	chr12:51156536..51158196-chr12:51316559..51318763,2	K562	blood:
11	chr12:51156477..51159239-chr12:51440349..51444629,5	K562	blood:
12	chr12:51155993..51157542-chr12:51233838..51236379,2	MCF-7	breast:
13	chr12:51156398..51158646-chr12:51422122..51423732,2	MCF-7	breast:
14	chr12:51156345..51159697-chr12:51418125..51424480,11	MCF-7	breast:
15	chr12:51155941..51160401-chr12:51475746..51478915,6	K562	blood:
16	chr12:50897453..50902823-chr12:51156009..51160960,8	MCF-7	breast:

No data

Variant related genes	Relation type
ATF1	TF binding region
ENSG00000110925	Chromatin interaction
ENSG00000066084	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000110934	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000185432	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000200428	Chromatin interaction
ENSG00000243075	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10459235	0.85[ASN][1000 genomes]
rs10506294	0.84[ASW][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap]
rs10506295	0.85[CHB][hapmap]
rs10747587	0.84[ASW][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap]
rs10783373	0.98[GIH][hapmap];0.86[MKK][hapmap]
rs10783382	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs10783384	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10783389	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876065	0.93[GIH][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap]
rs10876070	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs10876076	0.85[CHB][hapmap]
rs10876080	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876081	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876089	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876090	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876094	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876095	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876096	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876097	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169493	0.98[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs11169507	0.81[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap]
rs11169515	0.85[CHB][hapmap]
rs11169528	0.86[ASN][1000 genomes]
rs11169532	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11169537	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11169538	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11169539	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11169544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169554	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169560	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169561	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[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];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11613488	0.98[GIH][hapmap];0.83[MEX][hapmap]
rs11615933	0.84[ASN][1000 genomes]
rs12231309	0.85[CHB][hapmap]
rs12424860	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12809086	0.85[CHB][hapmap]
rs1344958	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17124930	0.84[CHB][hapmap]
rs35845404	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3742063	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3742064	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3809319	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3825402	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4026593	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4238108	0.85[CHB][hapmap]
rs4307773	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4768853	0.95[GIH][hapmap];0.83[MEX][hapmap]
rs4768893	0.84[ASW][hapmap]
rs4768903	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs4768906	0.86[ASN][1000 genomes]
rs4768907	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4768911	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4768912	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4768913	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4768914	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4768917	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768921	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768922	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4768923	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768924	1.00[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs4768925	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs4768940	0.80[EUR][1000 genomes]
rs73094900	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73096846	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs864899	0.86[CHB][hapmap]
rs876078	0.84[ASW][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap]
rs952318	0.81[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap]

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	esv3497481	chr12:51150734-51185125	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
2	esv3497482	chr12:51151798-51185232	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
3	esv3386327	chr12:51154734-51184232	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4768866	LASS5	cis	cerebellum	SCAN
rs4768866	DIP2B	cis	Thyroid	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51141800-51156600	Weak transcription	Fetal Brain Female	brain
2	chr12:51141800-51156800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr12:51142000-51156800	Weak transcription	Pancreas	Pancrea
4	chr12:51142200-51156800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr12:51142200-51156800	Weak transcription	Spleen	Spleen
6	chr12:51144600-51156800	Weak transcription	Lung	lung
7	chr12:51145000-51156800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:51146000-51156800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:51149000-51157000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:51154400-51156800	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:51154600-51156600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:51155200-51156600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:51155200-51156800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:51155600-51156800	Flanking Active TSS	Hela-S3	cervix
15	chr12:51155600-51159600	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr12:51155800-51158600	Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr12:51155800-51159400	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr12:51156000-51156600	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr12:51156000-51156600	Flanking Active TSS	A549	lung
20	chr12:51156000-51156800	Enhancers	Thymus	Thymus
21	chr12:51156000-51157200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr12:51156000-51157200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:51156000-51157200	Flanking Active TSS	Dnd41	blood
24	chr12:51156000-51157400	Active TSS	Right Atrium	heart
25	chr12:51156000-51158800	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr12:51156000-51159200	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr12:51156000-51159200	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr12:51156000-51159200	Active TSS	Left Ventricle	heart
29	chr12:51156000-51159600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr12:51156000-51159600	Active TSS	Colonic Mucosa	Colon
31	chr12:51156000-51159600	Active TSS	Right Ventricle	heart
32	chr12:51156000-51159600	Active TSS	K562	blood
33	chr12:51156200-51156600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:51156200-51156600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:51156200-51156600	Enhancers	Primary T cells from cord blood	blood
36	chr12:51156200-51156600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:51156200-51156600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:51156200-51156600	Enhancers	Brain Germinal Matrix	brain
39	chr12:51156200-51156600	Enhancers	Colon Smooth Muscle	Colon
40	chr12:51156200-51156600	Flanking Active TSS	Fetal Heart	heart
41	chr12:51156200-51156600	Enhancers	HMEC	breast
42	chr12:51156200-51156600	Enhancers	NHEK	skin
43	chr12:51156200-51156800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:51156200-51156800	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr12:51156200-51156800	Enhancers	Primary B cells from cord blood	blood
46	chr12:51156200-51156800	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr12:51156200-51156800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:51156200-51156800	Enhancers	Adipose Nuclei	Adipose
49	chr12:51156200-51156800	Active TSS	Brain Cingulate Gyrus	brain
50	chr12:51156200-51156800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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