Variant report

Variant	rs12752855
Chromosome Location	chr1:247043461-247043462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr1:247043390-247043580	HepG2	liver:	n/a	chr1:247043452-247043467
2	MAFK	chr1:247043332-247043591	HepG2	liver:	n/a	chr1:247043452-247043467

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247039071..247040788-chr1:247042685..247044930,2	K562	blood:
2	chr1:247041147..247045524-chr1:247051435..247055344,4	K562	blood:

Variant related genes	Relation type
AHCTF1	TF binding region
ENSG00000153207	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10436931	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10924862	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10924863	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10924866	0.81[CEU][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs10924867	0.81[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs10924868	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10924869	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11585265	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12023594	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12029050	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12032354	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12033144	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12033829	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12691532	0.90[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12728361	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12739487	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12739603	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12748665	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1892116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2067916	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35716055	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6426191	0.89[CHB][hapmap];0.93[JPT][hapmap]
rs7551797	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1810844	chr1:246988018-247054824	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv5276	chr1:247028364-247073098	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12752855	AHCTF1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247002200-247082400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:247002400-247081000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr1:247003400-247044600	Strong transcription	Dnd41	blood
4	chr1:247004000-247053600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:247004200-247044400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:247004200-247044400	Strong transcription	Liver	Liver
7	chr1:247004200-247083400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:247004400-247044600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:247005200-247079800	Weak transcription	Stomach Mucosa	stomach
10	chr1:247006600-247071600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:247018400-247056400	Weak transcription	Fetal Heart	heart
12	chr1:247020400-247072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:247024200-247052000	Weak transcription	Pancreas	Pancrea
14	chr1:247025200-247048000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:247025200-247052000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:247031200-247043800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:247031600-247071400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:247032400-247044400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:247032800-247051600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:247033200-247060800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:247033600-247058000	Weak transcription	Colonic Mucosa	Colon
22	chr1:247033800-247045000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:247033800-247046000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:247033800-247051600	Weak transcription	HSMMtube	muscle
25	chr1:247033800-247070800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:247035000-247051600	Weak transcription	Psoas Muscle	Psoas
27	chr1:247035800-247051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:247036200-247052000	Weak transcription	Small Intestine	intestine
29	chr1:247037200-247051800	Weak transcription	Brain Germinal Matrix	brain
30	chr1:247037400-247052000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:247038000-247050200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:247039000-247049000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:247039000-247051600	Weak transcription	Spleen	Spleen
34	chr1:247039000-247057200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:247039000-247070400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:247039200-247044000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:247039200-247047600	Weak transcription	Fetal Brain Female	brain
38	chr1:247039200-247050000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:247039200-247051600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:247039200-247051600	Weak transcription	Lung	lung
41	chr1:247039200-247052000	Weak transcription	Fetal Brain Male	brain
42	chr1:247039200-247052000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:247039400-247051400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:247039400-247052000	Weak transcription	Esophagus	oesophagus
45	chr1:247039800-247051400	Weak transcription	Right Ventricle	heart
46	chr1:247040200-247045800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:247040200-247050600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:247040200-247050800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:247040400-247045800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:247040400-247046000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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