Variant report

Variant	rs2669166
Chromosome Location	chr12:122149731-122149732
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:122149615-122149787	HepG2	liver:	n/a	n/a
2	ELF1	chr12:122149639-122149872	K562	blood:	n/a	chr12:122149778-122149791

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122148895..122150482-chr12:122213569..122215143,2	K562	blood:
2	chr12:122148985..122154094-chr12:122210649..122217008,11	MCF-7	breast:
3	chr12:122149249..122152147-chr12:122229581..122233327,7	MCF-7	breast:
4	chr12:122148639..122153380-chr12:122238008..122242328,5	MCF-7	breast:
5	chr12:122149069..122151072-chr12:122242291..122244324,2	MCF-7	breast:
6	chr12:122147215..122155218-chr12:122185094..122190846,22	MCF-7	breast:
7	chr12:122145450..122152863-chr12:122233897..122241914,16	MCF-7	breast:
8	chr12:122016960..122018583-chr12:122148688..122150222,2	K562	blood:

No data

Variant related genes	Relation type
TMEM120B	TF binding region
ENSG00000089094	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000139718	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10743188	0.81[EUR][1000 genomes]
rs11043179	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11043180	0.83[AMR][1000 genomes]
rs12320939	0.94[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap]
rs1877484	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2137434	0.84[MEX][hapmap]
rs2309142	0.82[AMR][1000 genomes]
rs2458404	0.91[GIH][hapmap]
rs2466145	0.84[MEX][hapmap]
rs2669163	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2669165	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2669168	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720021	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2720022	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2720025	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2720035	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720041	0.83[MEX][hapmap]
rs2942368	1.00[ASW][hapmap];0.85[CEU][hapmap];0.98[GIH][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2942379	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2954116	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3825175	0.94[ASW][hapmap];0.82[CEU][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap]
rs3934658	0.88[ASW][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs7135617	0.85[TSI][hapmap]
rs7399127	0.88[ASW][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs7967415	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs7978866	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122142600-122149800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:122142800-122149800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:122146400-122149800	Enhancers	Fetal Intestine Small	intestine
4	chr12:122147400-122149800	Enhancers	Fetal Muscle Leg	muscle
5	chr12:122148000-122149800	Enhancers	Fetal Muscle Trunk	muscle
6	chr12:122148000-122149800	Weak transcription	HSMMtube	muscle
7	chr12:122148200-122149800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:122148200-122149800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:122148200-122149800	Weak transcription	NH-A	brain
10	chr12:122148600-122150000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:122148800-122149800	Enhancers	Primary B cells from cord blood	blood
12	chr12:122149000-122149800	Weak transcription	GM12878-XiMat	blood
13	chr12:122149000-122150000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:122149200-122149800	Enhancers	Placenta	Placenta
15	chr12:122149200-122149800	Enhancers	Fetal Thymus	thymus
16	chr12:122149200-122149800	Enhancers	Psoas Muscle	Psoas
17	chr12:122149200-122150000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:122149200-122150000	Enhancers	Spleen	Spleen
19	chr12:122149400-122149800	Enhancers	Primary B cells from peripheral blood	blood
20	chr12:122149400-122149800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:122149400-122149800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:122149400-122149800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr12:122149400-122149800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:122149400-122149800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr12:122149400-122149800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr12:122149400-122149800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:122149400-122149800	Enhancers	Brain Substantia Nigra	brain
28	chr12:122149400-122149800	Enhancers	Colon Smooth Muscle	Colon
29	chr12:122149400-122149800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr12:122149400-122149800	Enhancers	Fetal Stomach	stomach
31	chr12:122149400-122149800	Enhancers	A549	lung
32	chr12:122149400-122149800	Enhancers	Dnd41	blood
33	chr12:122149400-122149800	Flanking Active TSS	HepG2	liver
34	chr12:122149400-122149800	Enhancers	K562	blood
35	chr12:122149400-122149800	Enhancers	NHEK	skin
36	chr12:122149400-122150000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:122149400-122150000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr12:122149400-122150000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr12:122149400-122150200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr12:122149400-122150200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr12:122149400-122150200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr12:122149400-122150400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr12:122149400-122150400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr12:122149400-122150400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:122149400-122150400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr12:122149400-122150400	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr12:122149400-122151800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:122149600-122149800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:122149600-122149800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:122149600-122149800	Enhancers	HUES48 Cell Line	embryonic stem cell

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