Variant report

Variant	rs12403415
Chromosome Location	chr1:246999707-246999708
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	BCL3	chr1:246999639-247002277	A549	lung:	n/a	chr1:247001916-247001925
2	STAT3	chr1:246999455-246999854	MCF10A-Er-Src	breast:	n/a	chr1:246999692-246999703
3	STAT3	chr1:246999539-247000052	MCF10A-Er-Src	breast:	n/a	chr1:246999692-246999703
4	MYC	chr1:246999379-247000244	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:246999486-247002141	MCF-7	breast:	n/a	n/a
6	GATA2	chr1:246999422-246999846	SH-SY5Y	brain:	n/a	n/a
7	POLR2A	chr1:246999482-247002222	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr1:246999453-247000389	SK-N-MC	brain:	n/a	n/a
9	STAT3	chr1:246999568-246999825	MCF10A-Er-Src	breast:	n/a	chr1:246999692-246999703
10	FOS	chr1:246999654-246999827	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr1:246999651-247000085	MCF10A-Er-Src	breast:	n/a	chr1:246999692-246999703
12	FOS	chr1:246999430-246999944	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr1:246999476-247000235	MCF10A-Er-Src	breast:	n/a	n/a
14	GATA3	chr1:246999354-246999755	SH-SY5Y	brain:	n/a	n/a
15	MYC	chr1:246999504-246999902	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:246999544-246999873	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:246999563-246999748	SK-N-SH	brain:	n/a	n/a
18	FOS	chr1:246999563-246999808	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:246999618-246999749	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr1:246999499-247001898	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr1:246999445-247000110	U87	brain:	n/a	n/a
22	CEBPB	chr1:246999704-247000336	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:246999483-246999826	H1-neurons	neurons:	n/a	n/a
24	REST	chr1:246999434-246999852	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246999464..247001183-chr1:247004017..247007456,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252011	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10802451	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10924861	0.90[CEU][hapmap]
rs11576429	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12031687	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12048921	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12401831	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12401878	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12410563	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28727999	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4971286	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55783683	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56070865	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61853987	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61853988	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61853995	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9633321	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
rs12403415	AHCTF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246989200-247011200	Weak transcription	Fetal Kidney	kidney
2	chr1:246993200-247004200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:246994800-247003200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:246995200-247001400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:246995400-247004200	Weak transcription	HUVEC	blood vessel
6	chr1:246997400-247002200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:246998800-247004200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:246999000-246999800	Enhancers	Ovary	ovary
9	chr1:246999000-247002400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr1:246999200-247004600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:246999200-247010000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:246999400-247001200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:246999400-247004000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:246999400-247004200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:246999600-246999800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:246999600-246999800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:246999600-246999800	Enhancers	Right Ventricle	heart
18	chr1:246999600-246999800	Active TSS	Hela-S3	cervix
19	chr1:246999600-247000200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:246999600-247000200	Enhancers	NHEK	skin
21	chr1:246999600-247001000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:246999600-247001400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:246999600-247001800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr1:246999600-247004400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:246999600-247004600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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