Variant report

Variant	rs12426862
Chromosome Location	chr12:104520054-104520055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104512826..104514662-chr12:104519104..104521337,2	K562	blood:
2	chr12:104513301..104516062-chr12:104519027..104521801,2	MCF-7	breast:
3	chr12:104515821..104520913-chr12:104521669..104524751,4	K562	blood:

Variant related genes	Relation type
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10507174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10507175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11831030	1.00[YRI][hapmap]
rs12422505	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]
rs12423684	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12423844	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]
rs12424943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12427339	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	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12582966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12825521	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]
rs17035324	0.85[CHB][hapmap]
rs17192854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17805748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17805766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35142441	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812800	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3850022	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4129598	0.85[CHB][hapmap]
rs4131750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4131752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4246264	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs4340124	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4388968	0.85[CEU][hapmap]
rs4545635	0.85[CHB][hapmap]
rs4614534	0.85[CHB][hapmap]
rs4964219	0.90[ASN][1000 genomes]
rs4964227	0.81[CEU][hapmap]
rs4964228	0.81[CEU][hapmap]
rs4964260	0.85[CHB][hapmap]
rs4964627	0.81[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes]
rs4964632	0.80[AMR][1000 genomes]
rs59079741	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59644448	0.90[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	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61937642	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61939180	0.82[ASN][1000 genomes]
rs61939183	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61939188	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61939190	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61939192	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61939195	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61939196	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61939198	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61939199	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61939200	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61939201	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7132418	0.81[CEU][hapmap]
rs7299866	0.85[CHB][hapmap];0.80[AMR][1000 genomes]
rs73177987	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73177991	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7957725	0.81[CEU][hapmap]
rs7975161	0.85[CHB][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	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12426862	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	chr12:104460000-104526200	Weak transcription	Colonic Mucosa	Colon
2	chr12:104493800-104530600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:104494400-104521000	Weak transcription	Lung	lung
4	chr12:104494400-104521200	Weak transcription	Aorta	Aorta
5	chr12:104494400-104522600	Weak transcription	Spleen	Spleen
6	chr12:104495600-104530800	Weak transcription	Esophagus	oesophagus
7	chr12:104497000-104524600	Weak transcription	Pancreas	Pancrea
8	chr12:104502800-104526200	Weak transcription	Psoas Muscle	Psoas
9	chr12:104507200-104528000	Strong transcription	Placenta	Placenta
10	chr12:104508000-104527000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr12:104508000-104528800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:104508200-104525000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:104508200-104525400	Strong transcription	Dnd41	blood
14	chr12:104508200-104525600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:104508200-104526200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr12:104508200-104526800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:104508200-104529200	Strong transcription	Fetal Thymus	thymus
18	chr12:104508400-104528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:104508600-104529000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:104509000-104528600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:104509600-104527000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:104509800-104528600	Weak transcription	Small Intestine	intestine
23	chr12:104510000-104521600	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:104510000-104524600	Weak transcription	Fetal Brain Male	brain
25	chr12:104510000-104524600	Weak transcription	Stomach Mucosa	stomach
26	chr12:104510200-104526000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:104510600-104524000	Strong transcription	Adipose Nuclei	Adipose
28	chr12:104510600-104524600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:104510600-104527000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:104510800-104527200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr12:104510800-104528600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:104511000-104520600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:104511200-104523600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:104511400-104525600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:104511600-104523200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr12:104512600-104522600	Weak transcription	Brain Angular Gyrus	brain
37	chr12:104513400-104524400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr12:104513400-104526200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:104513800-104524200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr12:104513800-104527400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:104513800-104528200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:104514000-104523000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr12:104514000-104524400	Strong transcription	Fetal Lung	lung
44	chr12:104514600-104520600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:104515000-104521200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:104515000-104526000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:104515400-104522800	Weak transcription	Brain Substantia Nigra	brain
48	chr12:104515600-104523400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr12:104515600-104527800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:104515600-104529200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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