Variant report

Variant	rs12427339
Chromosome Location	chr12:104524817-104524818
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	FOXA2	chr12:104524585-104525060	A549	lung:	n/a	n/a
2	FOXA1	chr12:104524532-104524908	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104520948..104523918-chr12:104524437..104526764,3	MCF-7	breast:
2	chr12:104515519..104518229-chr12:104522556..104526007,3	MCF-7	breast:
3	chr12:104322442..104325161-chr12:104524149..104527737,3	K562	blood:

Variant related genes	Relation type
NFYB	TF binding region
ENSG00000265072	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000214198	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10507174	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10507175	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778309	0.90[CHD][hapmap]
rs11111898	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12422505	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423684	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423844	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424943	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12426862	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579268	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12582966	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12825521	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035324	0.80[CHD][hapmap]
rs17192854	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17805748	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17805766	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17806643	0.82[CHD][hapmap]
rs35142441	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812800	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3850022	0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs4129598	0.85[CEU][hapmap];0.80[CHD][hapmap]
rs4131750	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[MEX][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4131752	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4340124	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4614534	0.85[CEU][hapmap];0.80[CHD][hapmap]
rs4964219	0.90[ASN][1000 genomes]
rs4964627	0.85[CEU][hapmap]
rs59079741	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59644448	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61647968	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61937639	0.97[ASN][1000 genomes]
rs61937641	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61937642	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61939180	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61939183	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61939188	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61939190	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61939192	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61939195	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61939196	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61939198	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61939199	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61939200	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61939201	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7132418	0.85[CEU][hapmap]
rs7294997	0.82[CEU][hapmap]
rs7299866	0.85[CEU][hapmap];0.82[CHD][hapmap]
rs73177987	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73177991	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7957725	0.85[CEU][hapmap]
rs7979648	0.95[CHD][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap]

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	esv1823607	chr12:104506318-104549541	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
2	esv1816017	chr12:104510676-104531860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
3	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
4	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12427339	NFYB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104460000-104526200	Weak transcription	Colonic Mucosa	Colon
2	chr12:104493800-104530600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:104495600-104530800	Weak transcription	Esophagus	oesophagus
4	chr12:104502800-104526200	Weak transcription	Psoas Muscle	Psoas
5	chr12:104507200-104528000	Strong transcription	Placenta	Placenta
6	chr12:104508000-104527000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:104508000-104528800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:104508200-104525000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:104508200-104525400	Strong transcription	Dnd41	blood
10	chr12:104508200-104525600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:104508200-104526200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr12:104508200-104526800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr12:104508200-104529200	Strong transcription	Fetal Thymus	thymus
14	chr12:104508400-104528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:104508600-104529000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:104509000-104528600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:104509600-104527000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:104509800-104528600	Weak transcription	Small Intestine	intestine
19	chr12:104510200-104526000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:104510600-104527000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:104510800-104527200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:104510800-104528600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:104511400-104525600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:104513400-104526200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:104513800-104527400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:104513800-104528200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:104515000-104526000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr12:104515600-104527800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:104515600-104529200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:104515800-104528800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:104515800-104529200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr12:104516000-104526200	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:104516400-104525000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:104516400-104525000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:104516400-104528000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:104516600-104528200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:104516600-104528800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:104517000-104526800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:104517600-104527000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:104518000-104527400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:104518800-104525400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:104519600-104526200	Weak transcription	Gastric	stomach
43	chr12:104519800-104528800	Strong transcription	Primary B cells from cord blood	blood
44	chr12:104520000-104530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:104520600-104525600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:104520600-104527800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:104520800-104525200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:104521000-104528800	Weak transcription	Hela-S3	cervix
49	chr12:104521400-104528600	Strong transcription	Thymus	Thymus
50	chr12:104521800-104525400	Weak transcription	Right Ventricle	heart

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