Variant report

Variant	rs12031687
Chromosome Location	chr1:247004392-247004393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246991725..246994648-chr1:247001780..247004599,2	K562	blood:
2	chr1:247001934..247004833-chr1:247007258..247009999,3	K562	blood:
3	chr1:246999464..247001183-chr1:247004017..247007456,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223519	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10802451	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10924861	0.80[EUR][1000 genomes]
rs11576429	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12048921	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12401831	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12401878	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12403415	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12410563	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28727999	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971286	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55783683	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56070865	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61853987	0.84[EUR][1000 genomes]
rs61853988	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61853995	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9633321	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12031687	AHCTF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246989200-247011200	Weak transcription	Fetal Kidney	kidney
2	chr1:246999200-247004600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:246999200-247010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:246999600-247004400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:246999600-247004600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:246999800-247004400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:246999800-247004400	Weak transcription	Hela-S3	cervix
8	chr1:246999800-247005600	Weak transcription	Ovary	ovary
9	chr1:246999800-247007600	Weak transcription	Right Ventricle	heart
10	chr1:247000200-247004400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:247000200-247004400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:247000200-247020200	Weak transcription	Spleen	Spleen
13	chr1:247000600-247004600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:247000600-247007800	Weak transcription	Fetal Brain Female	brain
15	chr1:247000800-247004400	Weak transcription	Left Ventricle	heart
16	chr1:247000800-247004600	Weak transcription	Primary B cells from cord blood	blood
17	chr1:247001000-247006200	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:247001200-247004400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:247001400-247004400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:247001400-247004400	Weak transcription	Brain Angular Gyrus	brain
21	chr1:247001400-247012000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:247001400-247016400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:247001400-247020000	Weak transcription	Brain Substantia Nigra	brain
24	chr1:247001600-247004400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:247001600-247004400	Weak transcription	GM12878-XiMat	blood
26	chr1:247001600-247004400	Weak transcription	HMEC	breast
27	chr1:247001600-247004400	Weak transcription	K562	blood
28	chr1:247001800-247004400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:247001800-247004400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:247002000-247004600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:247002000-247038200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:247002200-247031400	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:247002200-247033800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:247002200-247034200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:247002200-247082400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr1:247002400-247004400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:247002400-247005400	Weak transcription	Thymus	Thymus
38	chr1:247002400-247081000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:247002600-247004400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:247002600-247004400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:247002600-247004400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:247002600-247004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:247002600-247004400	Weak transcription	Adipose Nuclei	Adipose
44	chr1:247002600-247004400	Weak transcription	Brain Anterior Caudate	brain
45	chr1:247002600-247004400	Weak transcription	Brain Germinal Matrix	brain
46	chr1:247002600-247004400	Weak transcription	Fetal Lung	lung
47	chr1:247002600-247004600	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:247002800-247004400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:247002800-247006000	Weak transcription	HepG2	liver
50	chr1:247002800-247006200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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