Variant report

Variant	rs10880942
Chromosome Location	chr12:46619130-46619131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46618654..46626602-chr12:46659026..46664546,12	MCF-7	breast:
2	chr12:46618211..46621572-chr12:46623361..46625417,5	K562	blood:

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10160965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10219550	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs10880936	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880940	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183397	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12307102	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822740	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1822741	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2125644	0.81[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs57668910	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58776177	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7953774	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7965237	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7971883	0.81[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7975060	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7980222	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963325	1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46592800-46654200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:46597600-46659600	Weak transcription	Colonic Mucosa	Colon
3	chr12:46604000-46623400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:46604000-46633800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:46604000-46637400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:46610400-46624000	Weak transcription	Pancreas	Pancrea
7	chr12:46610600-46640000	Weak transcription	Esophagus	oesophagus
8	chr12:46613200-46619200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:46613200-46619600	Enhancers	Colon Smooth Muscle	Colon
10	chr12:46613200-46619800	Genic enhancers	Primary B cells from peripheral blood	blood
11	chr12:46613400-46619600	Genic enhancers	Primary B cells from cord blood	blood
12	chr12:46613400-46621400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:46613800-46639800	Weak transcription	Lung	lung
14	chr12:46614000-46624200	Weak transcription	Fetal Brain Male	brain
15	chr12:46614200-46619400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr12:46614400-46621600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:46614400-46627400	Weak transcription	Right Ventricle	heart
18	chr12:46614600-46619800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:46615200-46619200	Weak transcription	Fetal Intestine Small	intestine
20	chr12:46615600-46632400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:46615600-46636600	Weak transcription	Brain Anterior Caudate	brain
22	chr12:46615800-46619600	Strong transcription	HSMM	muscle
23	chr12:46615800-46621600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:46615800-46623600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:46615800-46637800	Weak transcription	Dnd41	blood
26	chr12:46615800-46653800	Weak transcription	NH-A	brain
27	chr12:46616000-46640600	Strong transcription	Fetal Thymus	thymus
28	chr12:46616000-46650400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:46616200-46619400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:46616200-46621400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:46616200-46621400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:46616200-46636600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:46616400-46620200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr12:46616400-46620200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:46616400-46637200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:46616400-46637800	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:46616400-46653600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:46616600-46619800	Strong transcription	A549	lung
39	chr12:46616800-46619600	Genic enhancers	Primary T cells from cord blood	blood
40	chr12:46616800-46619600	Strong transcription	Placenta	Placenta
41	chr12:46616800-46627200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:46616800-46638600	Strong transcription	HMEC	breast
43	chr12:46616800-46639800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:46616800-46641600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:46617000-46619400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr12:46617000-46619600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr12:46617000-46619600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr12:46617000-46636800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:46617000-46637800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr12:46617000-46653000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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