Variant report

Variant	rs12423844
Chromosome Location	chr12:104526054-104526055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr12:104526043-104526712	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr12:104526045-104526544	T-47D	breast:	n/a	n/a
3	MXI1	chr12:104525157-104527002	SK-N-SH	brain:	n/a	n/a
4	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
ENSG00000214198	Chromatin interaction
ENSG00000199415	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000265072	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10507174	1.00[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	1.00[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	1.00[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]
rs12422505	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]
rs12423684	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12424943	1.00[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	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]
rs12579268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12582966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12825521	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]
rs17035324	0.85[CHB][hapmap]
rs17192854	1.00[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	1.00[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	1.00[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[CEU][hapmap];0.85[CHB][hapmap]
rs4131750	1.00[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	1.00[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	1.00[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[CEU][hapmap];0.85[CHB][hapmap]
rs4964219	0.90[ASN][1000 genomes]
rs4964260	0.85[CHB][hapmap]
rs4964627	0.86[CEU][hapmap];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]
rs7132418	0.86[CEU][hapmap]
rs7294997	0.82[CEU][hapmap]
rs7299866	0.85[CEU][hapmap];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]
rs7957725	0.86[CEU][hapmap]
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
rs12423844	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	chr12:104495600-104530800	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	chr12:104508200-104526200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr12:104508200-104526800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:104508200-104529200	Strong transcription	Fetal Thymus	thymus
11	chr12:104508400-104528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:104508600-104529000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:104509000-104528600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:104509600-104527000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:104509800-104528600	Weak transcription	Small Intestine	intestine
16	chr12:104510600-104527000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:104510800-104527200	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:104510800-104528600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:104513400-104526200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:104513800-104527400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:104513800-104528200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr12:104515600-104527800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:104515600-104529200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:104515800-104528800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:104515800-104529200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr12:104516000-104526200	Strong transcription	Fetal Muscle Leg	muscle
27	chr12:104516400-104528000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:104516600-104528200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:104516600-104528800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:104517000-104526800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:104517600-104527000	Strong transcription	Primary hematopoietic stem cells	blood
32	chr12:104518000-104527400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:104519600-104526200	Weak transcription	Gastric	stomach
34	chr12:104519800-104528800	Strong transcription	Primary B cells from cord blood	blood
35	chr12:104520000-104530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:104520600-104527800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:104521000-104528800	Weak transcription	Hela-S3	cervix
38	chr12:104521400-104528600	Strong transcription	Thymus	Thymus
39	chr12:104521800-104526200	Weak transcription	Lung	lung
40	chr12:104522000-104527200	Strong transcription	HMEC	breast
41	chr12:104522600-104528200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:104523600-104526200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:104523600-104526400	Weak transcription	HUVEC	blood vessel
44	chr12:104523600-104527600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr12:104523600-104530600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:104523800-104528200	Enhancers	Liver	Liver
47	chr12:104523800-104529800	Weak transcription	Fetal Intestine Small	intestine
48	chr12:104523800-104530400	Enhancers	Fetal Heart	heart
49	chr12:104523800-104530600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr12:104524000-104526200	Enhancers	Rectal Smooth Muscle	rectum

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