Variant report

Variant	rs12580097
Chromosome Location	chr12:51500886-51500887
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51473248..51478369-chr12:51498942..51502935,5	MCF-7	breast:
2	chr12:51474348..51478730-chr12:51495114..51501288,7	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LETMD1-1	chr12:51500600-51500927	NONHSAT028239

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12582592	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17122760	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17125258	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17125286	0.94[EUR][1000 genomes]
rs17125346	0.96[EUR][1000 genomes]
rs17125369	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125375	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125401	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3759406	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4768876	0.84[EUR][1000 genomes]
rs55679918	0.84[EUR][1000 genomes]
rs55864652	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55897461	0.94[EUR][1000 genomes]
rs55987825	0.93[EUR][1000 genomes]
rs56060103	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56335028	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56847302	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60910794	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67466786	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67478184	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73103154	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73105025	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979705	0.95[ASN][1000 genomes]

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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv973065	chr12:51500579-51501168	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12580097	TFCP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477400-51518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51477800-51518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:51477800-51518400	Weak transcription	Pancreas	Pancrea
4	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:51483800-51513400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:51484000-51502000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:51484400-51506000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr12:51484800-51507000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:51485000-51507600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr12:51485000-51513200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:51485800-51513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:51486000-51511400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:51486400-51510800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:51486600-51508000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:51486800-51504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:51486800-51508000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr12:51487000-51505000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:51487000-51506600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:51487000-51511400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:51487200-51502000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:51487200-51505000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:51487200-51508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:51487200-51513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:51487200-51513200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:51487400-51511000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:51487600-51504800	Strong transcription	Adipose Nuclei	Adipose
28	chr12:51487600-51508200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr12:51487600-51512000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr12:51487800-51505000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:51487800-51505600	Strong transcription	Liver	Liver
32	chr12:51488000-51507600	Strong transcription	Fetal Intestine Large	intestine
33	chr12:51488400-51526600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:51489200-51509400	Weak transcription	Fetal Heart	heart
35	chr12:51493600-51501200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:51493600-51512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:51494000-51503000	Weak transcription	Brain Angular Gyrus	brain
38	chr12:51494200-51501800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:51494400-51515600	Weak transcription	Stomach Mucosa	stomach
40	chr12:51494600-51502200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr12:51494600-51518200	Weak transcription	Esophagus	oesophagus
42	chr12:51494800-51518400	Weak transcription	Aorta	Aorta
43	chr12:51495000-51504000	Weak transcription	Gastric	stomach
44	chr12:51496400-51523400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:51497000-51504600	Strong transcription	Hela-S3	cervix
46	chr12:51497600-51502800	Weak transcription	Brain Germinal Matrix	brain
47	chr12:51498000-51504000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:51498800-51505000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:51499000-51501600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:51499000-51503600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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