Variant report

Variant	rs1538257
Chromosome Location	chr14:55879277-55879278
allele	A/C
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	POLR2A	chr14:55877995-55879786	Hela-S3	cervix:	n/a	n/a
2	NR2F2	chr14:55879245-55879860	MCF-7	breast:	n/a	n/a
3	MXI1	chr14:55878345-55879732	Hela-S3	cervix:	n/a	chr14:55878561-55878570
4	POLR2A	chr14:55878182-55879368	Raji	blood:	n/a	n/a
5	NR2F2	chr14:55879175-55879957	MCF-7	breast:	n/a	n/a
6	GATA3	chr14:55878071-55880708	MCF-7	breast:	n/a	chr14:55878107-55878116
7	USF1	chr14:55879035-55879308	SK-N-SH_RA	brain:	n/a	n/a
8	FOXM1	chr14:55878232-55879785	MCF-7	breast:	n/a	n/a
9	MAX	chr14:55878204-55879797	MCF-7	breast:	n/a	chr14:55879180-55879193 chr14:55879182-55879191 chr14:55879771-55879779 chr14:55879180-55879193 chr14:55878562-55878571
10	EP300	chr14:55879273-55879808	MCF-7	breast:	n/a	n/a
11	MXI1	chr14:55878125-55879867	SK-N-SH	brain:	n/a	chr14:55878561-55878570
12	HCFC1	chr14:55877906-55880028	Hela-S3	cervix:	n/a	n/a
13	SIN3AK20	chr14:55878031-55879873	MCF-7	breast:	n/a	n/a
14	POLR2A	chr14:55878325-55879294	GM12891	blood:	n/a	n/a
15	USF2	chr14:55878374-55879697	Hela-S3	cervix:	n/a	chr14:55878560-55878571
16	POLR2A	chr14:55878228-55879540	HepG2	liver:	n/a	n/a
17	RCOR1	chr14:55878352-55879287	GM12878	blood:	n/a	n/a
18	POLR2A	chr14:55877900-55879293	K562	blood:	n/a	n/a
19	STAT3	chr14:55879174-55879572	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr14:55878102-55879772	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr14:55877644-55879780	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr14:55877896-55879679	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55878684..55880292-chr14:55881926..55883661,2	K562	blood:
2	chr14:55736296..55738259-chr14:55878149..55880015,2	MCF-7	breast:
3	chr14:55832090..55833883-chr14:55878712..55880700,2	MCF-7	breast:
4	chr14:55736665..55740457-chr14:55875135..55883763,10	K562	blood:

Variant related genes	Relation type
ATG14	TF binding region
ENSG00000178974	Chromatin interaction
ENSG00000258413	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1009648	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10134339	0.89[ASW][hapmap];0.86[MEX][hapmap]
rs10138446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10140801	0.82[MEX][hapmap]
rs1109170	0.89[ASW][hapmap];0.86[MEX][hapmap]
rs11624331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2009291	0.89[ASW][hapmap];0.86[MEX][hapmap]
rs2341622	0.89[ASW][hapmap];0.85[MEX][hapmap]
rs34727214	0.82[ASN][1000 genomes]
rs3783650	0.89[ASW][hapmap];0.86[MEX][hapmap]
rs4901562	0.87[YRI][hapmap]
rs6573009	0.85[MEX][hapmap]
rs6573013	0.89[ASW][hapmap];0.86[MEX][hapmap]
rs6573014	0.89[ASW][hapmap];0.86[MEX][hapmap]
rs7153110	0.89[ASW][hapmap];0.86[MEX][hapmap]
rs7153619	0.83[ASN][1000 genomes]
rs7156360	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7158768	0.89[ASW][hapmap];0.86[MEX][hapmap]
rs8010013	0.87[YRI][hapmap]
rs8014526	0.87[YRI][hapmap]
rs946055	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs946056	0.81[ASN][1000 genomes]
rs946057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs946059	0.89[ASW][hapmap];0.86[MEX][hapmap]

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	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv901959	chr14:55853724-55916225	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
4	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1538257	FBXO34	cis	cerebellum	SCAN
rs1538257	RP11-665C16.6	cis	Muscle Skeletal	GTEx
rs1538257	ATG14	cis	parietal	SCAN
rs1538257	TIMM9	cis	parietal	SCAN
rs1538257	WDHD1	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55877200-55879400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr14:55877400-55879400	Active TSS	Psoas Muscle	Psoas
3	chr14:55877600-55879400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr14:55878000-55879400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr14:55878000-55879400	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr14:55878600-55879400	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr14:55878600-55879400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr14:55878600-55879400	Flanking Active TSS	Dnd41	blood
9	chr14:55878600-55879600	Flanking Active TSS	HMEC	breast
10	chr14:55878800-55879400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr14:55878800-55879400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr14:55878800-55879400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr14:55878800-55879400	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr14:55878800-55879400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr14:55878800-55879400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:55878800-55879400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr14:55878800-55879400	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr14:55878800-55879400	Flanking Active TSS	K562	blood
19	chr14:55878800-55879400	Flanking Active TSS	Osteobl	bone
20	chr14:55878800-55879600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr14:55878800-55879600	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr14:55878800-55879600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr14:55878800-55879600	Flanking Active TSS	NHDF-Ad	bronchial
24	chr14:55878800-55879800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr14:55878800-55879800	Flanking Active TSS	Hela-S3	cervix
26	chr14:55878800-55880200	Flanking Active TSS	NHEK	skin
27	chr14:55879000-55879400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr14:55879000-55879400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr14:55879000-55879400	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr14:55879000-55879400	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr14:55879000-55879400	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr14:55879000-55879400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr14:55879000-55879400	Enhancers	Small Intestine	intestine
34	chr14:55879000-55879400	Flanking Active TSS	HepG2	liver
35	chr14:55879000-55879600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:55879000-55879600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr14:55879000-55879600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr14:55879000-55879600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr14:55879000-55879800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr14:55879000-55880200	Enhancers	Stomach Mucosa	stomach
41	chr14:55879200-55879400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr14:55879200-55879400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr14:55879200-55879400	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr14:55879200-55879400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr14:55879200-55879400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr14:55879200-55879400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr14:55879200-55879400	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr14:55879200-55879400	Enhancers	Primary B cells from peripheral blood	blood
49	chr14:55879200-55879400	Enhancers	Primary hematopoietic stem cells	blood
50	chr14:55879200-55879400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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