Variant report

Variant	rs12582592
Chromosome Location	chr12:51513608-51513609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51511432..51514405-chr12:51516355..51519343,3	K562	blood:
2	chr12:51508563..51511245-chr12:51513189..51515662,2	K562	blood:
3	chr12:51476509..51478783-chr12:51511633..51515177,3	MCF-7	breast:
4	chr12:51511756..51514256-chr12:51530375..51532854,2	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000257246	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11169689	0.81[CEU][hapmap]
rs11169691	0.81[CEU][hapmap]
rs12305170	0.82[JPT][hapmap]
rs12317171	0.82[JPT][hapmap]
rs12580097	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17122760	0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17125258	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17125286	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17125346	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs17125369	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17125375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17125401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224568	0.95[CHB][hapmap]
rs3751275	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs3759406	1.00[CEU][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4768876	0.84[EUR][1000 genomes]
rs4768948	0.82[JPT][hapmap]
rs55679918	0.84[EUR][1000 genomes]
rs55864652	0.92[AFR][1000 genomes];0.99[EUR][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];0.85[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];0.98[ASN][1000 genomes]
rs60910794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67466786	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67478184	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73103154	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73105025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979705	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.92[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12582592	TFCP2	cis	lymphoblastoid	seeQTL
rs12582592	TFCP2	cis	multi-tissue	Pritchard
rs12582592	TFCP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 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	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:51488400-51526600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:51494400-51515600	Weak transcription	Stomach Mucosa	stomach
8	chr12:51494600-51518200	Weak transcription	Esophagus	oesophagus
9	chr12:51494800-51518400	Weak transcription	Aorta	Aorta
10	chr12:51496400-51523400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:51501000-51517400	Weak transcription	Psoas Muscle	Psoas
12	chr12:51501000-51521000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:51501800-51518400	Weak transcription	Spleen	Spleen
14	chr12:51502200-51527200	Weak transcription	Colonic Mucosa	Colon
15	chr12:51502600-51518400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:51502800-51531800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:51503000-51518400	Weak transcription	NHLF	lung
18	chr12:51503200-51518600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:51503200-51560200	Weak transcription	Right Ventricle	heart
20	chr12:51503600-51532000	Weak transcription	Brain Angular Gyrus	brain
21	chr12:51504400-51518200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:51504400-51518400	Weak transcription	Ovary	ovary
23	chr12:51504800-51518200	Weak transcription	Gastric	stomach
24	chr12:51504800-51518600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:51504800-51518600	Weak transcription	Brain Substantia Nigra	brain
26	chr12:51504800-51518800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:51504800-51563400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:51505200-51518200	Weak transcription	Lung	lung
29	chr12:51507600-51519800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:51507800-51532200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:51507800-51539800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:51508000-51543000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:51508200-51518200	Weak transcription	Left Ventricle	heart
34	chr12:51508200-51518200	Weak transcription	HUVEC	blood vessel
35	chr12:51509600-51520800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:51509800-51518200	Weak transcription	Brain Germinal Matrix	brain
37	chr12:51509800-51518600	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:51510000-51516800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:51510200-51514000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:51510200-51516400	Weak transcription	Fetal Kidney	kidney
41	chr12:51510200-51518000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:51510200-51518000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:51510200-51518200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:51510200-51518400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:51510200-51518400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:51510200-51518600	Weak transcription	Brain Anterior Caudate	brain
47	chr12:51510200-51518600	Weak transcription	NHDF-Ad	bronchial
48	chr12:51510200-51519200	Weak transcription	Fetal Heart	heart
49	chr12:51510200-51520400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:51510200-51526000	Weak transcription	H9 Cell Line	embryonic stem cell

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