Variant report

Variant	rs1154407
Chromosome Location	chr4:100008332-100008333
allele	C/G
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	YY1	chr4:100008269-100008578	HepG2	liver:	n/a	chr4:100008542-100008553
2	ZNF384	chr4:100007956-100008389	K562	blood:	n/a	n/a
3	GTF3C2	chr4:100007945-100008672	K562	blood:	n/a	n/a
4	POLR2A	chr4:100008266-100008497	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr4:100008168-100008801	HepG2	liver:	n/a	n/a
6	CEBPB	chr4:100008196-100009601	K562	blood:	n/a	chr4:100009401-100009412 chr4:100009059-100009072 chr4:100009400-100009413 chr4:100008735-100008748 chr4:100009061-100009072
7	RCOR1	chr4:100008054-100008563	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:99914937..99918533-chr4:100007922..100010203,4	K562	blood:
2	chr4:99951373..99953005-chr4:100007401..100010388,2	MCF-7	breast:
3	chr4:100007607..100009144-chr4:100870095..100871989,2	K562	blood:
4	chr4:99915328..99918402-chr4:100008331..100011431,5	MCF-7	breast:
5	chr4:99849612..99852371-chr4:100007085..100010224,5	K562	blood:
6	chr4:99848192..99852255-chr4:100007586..100012546,7	K562	blood:
7	chr4:99849574..99853806-chr4:100008192..100011466,4	MCF-7	breast:

Variant related genes	Relation type
ADH5	TF binding region
ENSG00000246090	TF binding region
ENSG00000238449	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000263923	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000151247	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1133485	0.82[EUR][1000 genomes]
rs1154405	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1154406	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1154410	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12506256	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1311615	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311616	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311617	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311618	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1311619	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1377689	0.82[EUR][1000 genomes]
rs1453873	0.81[EUR][1000 genomes]
rs1453874	0.82[EUR][1000 genomes]
rs1840228	0.82[EUR][1000 genomes]
rs1840230	0.82[EUR][1000 genomes]
rs1840231	0.81[EUR][1000 genomes]
rs2034696	0.82[EUR][1000 genomes]
rs2602845	0.82[EUR][1000 genomes]
rs2602846	0.82[EUR][1000 genomes]
rs2602847	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602855	0.82[EUR][1000 genomes]
rs2602858	0.82[EUR][1000 genomes]
rs2602859	0.82[EUR][1000 genomes]
rs2851263	0.82[EUR][1000 genomes]
rs2851266	0.81[EUR][1000 genomes]
rs2851267	0.81[EUR][1000 genomes]
rs2851268	0.82[EUR][1000 genomes]
rs2851269	0.82[EUR][1000 genomes]
rs2851277	0.82[EUR][1000 genomes]
rs2851278	0.82[EUR][1000 genomes]
rs2851282	0.82[AMR][1000 genomes]
rs2851283	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2851286	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2924580	0.81[EUR][1000 genomes]
rs3018047	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3018048	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6532779	0.81[AMR][1000 genomes]
rs6822830	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6831225	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9761048	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv1849572	chr4:100007243-100024396	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1154407	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99977600-100008400	Weak transcription	Stomach Mucosa	stomach
2	chr4:99977800-100009000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:99983200-100008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:99998000-100008800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:100001600-100008600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:100002400-100008800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:100004000-100008600	Weak transcription	Brain Substantia Nigra	brain
8	chr4:100004800-100008800	Enhancers	Fetal Heart	heart
9	chr4:100005600-100008800	Weak transcription	Brain Angular Gyrus	brain
10	chr4:100005600-100009000	Weak transcription	Esophagus	oesophagus
11	chr4:100005600-100009200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:100005600-100009400	Weak transcription	Spleen	Spleen
13	chr4:100006200-100008800	Weak transcription	Brain Anterior Caudate	brain
14	chr4:100006200-100008800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:100006200-100009000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:100006200-100009000	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:100006200-100009200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:100006400-100008600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:100006600-100008400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:100006600-100008600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:100006600-100008800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:100006600-100011400	Active TSS	Colonic Mucosa	Colon
23	chr4:100006600-100012400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:100006800-100008400	Weak transcription	GM12878-XiMat	blood
25	chr4:100006800-100008600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr4:100006800-100008600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:100006800-100008600	Enhancers	Fetal Brain Male	brain
28	chr4:100006800-100008600	Enhancers	Small Intestine	intestine
29	chr4:100006800-100008800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr4:100006800-100008800	Weak transcription	Primary T cells from cord blood	blood
31	chr4:100006800-100008800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:100006800-100012400	Active TSS	NHLF	lung
33	chr4:100007000-100008400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:100007000-100008400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:100007000-100008400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:100007000-100008400	Weak transcription	Primary B cells from cord blood	blood
37	chr4:100007000-100008600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr4:100007000-100008600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:100007000-100008600	Active TSS	Rectal Smooth Muscle	rectum
40	chr4:100007000-100008800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr4:100007000-100008800	Weak transcription	Psoas Muscle	Psoas
42	chr4:100007000-100008800	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr4:100007000-100008800	Weak transcription	HSMMtube	muscle
44	chr4:100007000-100009000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:100007000-100009000	Enhancers	Primary T cells fromperipheralblood	blood
46	chr4:100007000-100009200	Weak transcription	Gastric	stomach
47	chr4:100007000-100009600	Active TSS	Aorta	Aorta
48	chr4:100007000-100011600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:100007000-100011600	Active TSS	Duodenum Mucosa	Duodenum
50	chr4:100007200-100008400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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