Variant report

Variant	rs12422505
Chromosome Location	chr12:104526295-104526296
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr12:104526076-104526679	HEK293-T-REx	kidney:	n/a	n/a
2	GATA2	chr12:104526043-104526712	SH-SY5Y	brain:	n/a	n/a
3	KAP1	chr12:104526174-104526804	HEK293	kidney:	n/a	n/a
4	GATA3	chr12:104526045-104526544	T-47D	breast:	n/a	n/a
5	MXI1	chr12:104525157-104527002	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr12:104526160-104526310	BE2_C	brain:	n/a	n/a
7	CTCF	chr12:104526200-104526350	BE2_C	brain:	n/a	n/a
8	GATA3	chr12:104526196-104526478	MCF-7	breast:	n/a	n/a
9	GATA3	chr12:104525892-104526674	SH-SY5Y	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104521909..104523534-chr12:104525227..104527669,2	MCF-7	breast:
2	chr12:104510515..104519727-chr12:104525085..104533754,15	MCF-7	breast:
3	chr12:104520948..104523918-chr12:104524437..104526764,3	MCF-7	breast:
4	chr12:104322442..104325161-chr12:104525155..104527737,2	K562	blood:
5	chr12:104322442..104325161-chr12:104524149..104527737,3	K562	blood:

No data

Variant related genes	Relation type
NFYB	TF binding region
ENSG00000120837	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000199415	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000214198	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10507174	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10507175	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111898	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423684	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424943	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12426862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427339	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]
rs12579268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12582966	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12825521	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035324	0.85[CHB][hapmap]
rs17192854	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17805748	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17805766	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35142441	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3850022	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4129598	0.85[CHB][hapmap]
rs4131750	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4131752	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4246264	0.85[CHB][hapmap]
rs4340124	0.93[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4545635	0.85[CHB][hapmap]
rs4614534	0.85[CHB][hapmap]
rs4964219	0.90[ASN][1000 genomes]
rs4964260	0.85[CHB][hapmap]
rs4964627	0.85[CHB][hapmap]
rs59079741	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59644448	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61647968	0.82[ASN][1000 genomes]
rs61937639	0.97[ASN][1000 genomes]
rs61937641	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61937642	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61939180	0.82[ASN][1000 genomes]
rs61939183	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61939188	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61939190	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61939192	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61939195	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61939196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61939198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61939199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61939200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61939201	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7294997	0.82[CEU][hapmap]
rs7299866	0.85[CHB][hapmap]
rs73177987	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73177991	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7975161	0.85[CHB][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
rs12422505	NFYB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104493800-104530600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:104495600-104530800	Weak transcription	Esophagus	oesophagus
3	chr12:104507200-104528000	Strong transcription	Placenta	Placenta
4	chr12:104508000-104527000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:104508000-104528800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:104508200-104526800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr12:104508200-104529200	Strong transcription	Fetal Thymus	thymus
8	chr12:104508400-104528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:104508600-104529000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:104509000-104528600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:104509600-104527000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:104509800-104528600	Weak transcription	Small Intestine	intestine
13	chr12:104510600-104527000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:104510800-104527200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr12:104510800-104528600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:104513800-104527400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:104513800-104528200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr12:104515600-104527800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:104515600-104529200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:104515800-104528800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:104515800-104529200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:104516400-104528000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:104516600-104528200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:104516600-104528800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:104517000-104526800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:104517600-104527000	Strong transcription	Primary hematopoietic stem cells	blood
27	chr12:104518000-104527400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:104519800-104528800	Strong transcription	Primary B cells from cord blood	blood
29	chr12:104520000-104530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:104520600-104527800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:104521000-104528800	Weak transcription	Hela-S3	cervix
32	chr12:104521400-104528600	Strong transcription	Thymus	Thymus
33	chr12:104522000-104527200	Strong transcription	HMEC	breast
34	chr12:104522600-104528200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:104523600-104526400	Weak transcription	HUVEC	blood vessel
36	chr12:104523600-104527600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:104523600-104530600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:104523800-104528200	Enhancers	Liver	Liver
39	chr12:104523800-104529800	Weak transcription	Fetal Intestine Small	intestine
40	chr12:104523800-104530400	Enhancers	Fetal Heart	heart
41	chr12:104523800-104530600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:104524200-104526600	Enhancers	HepG2	liver
43	chr12:104524200-104527000	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr12:104524200-104527200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:104524400-104526400	Enhancers	Brain Angular Gyrus	brain
46	chr12:104524400-104526600	Genic enhancers	Fetal Lung	lung
47	chr12:104524400-104527000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr12:104524600-104526400	Genic enhancers	Fetal Stomach	stomach
49	chr12:104524800-104527800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:104524800-104529000	Strong transcription	Fetal Intestine Large	intestine

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