Variant report

Variant	rs1154403
Chromosome Location	chr4:100009590-100009591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:183)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:183 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr4:100009565-100010330	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:100009569-100010278	HCT-116	colon:	n/a	n/a
3	POLR2A	chr4:100009487-100010457	GM12878	blood:	n/a	n/a
4	MAX	chr4:100009544-100010466	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:100009342-100010774	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYC	chr4:100009260-100009605	MCF10A-Er-Src	breast:	n/a	n/a
7	YY1	chr4:100009486-100010283	H1-hESC	embryonic stem cell:	n/a	chr4:100009843-100009855
8	TAF1	chr4:100009345-100010312	H1-neurons	neurons:	n/a	n/a
9	TAF7	chr4:100009161-100010305	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr4:100009417-100010468	GM19193	blood:	n/a	n/a
11	POLR2A	chr4:100009460-100010561	GM12892	blood:	n/a	n/a
12	YY1	chr4:100009413-100010497	SK-N-SH	brain:	n/a	chr4:100009843-100009855
13	HA-E2F1	chr4:100009119-100010991	MCF-7	breast:	n/a	chr4:100009757-100009766
14	MAZ	chr4:100009016-100010655	IMR90	lung:	n/a	n/a
15	POLR2A	chr4:100009353-100010502	MCF-7	breast:	n/a	n/a
16	JUN	chr4:100009427-100010419	K562	blood:	n/a	chr4:100009569-100009578
17	POLR2A	chr4:100009187-100010796	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr4:100009300-100010440	K562	blood:	n/a	n/a
19	POLR2A	chr4:100009343-100010422	Hela-S3	cervix:	n/a	n/a
20	TCF12	chr4:100009458-100010650	A549	lung:	n/a	n/a
21	POLR2A	chr4:100009578-100010185	A549	lung:	n/a	n/a
22	TBP	chr4:100009240-100010666	GM12878	blood:	n/a	n/a
23	POLR2A	chr4:100009211-100010921	HepG2	liver:	n/a	n/a
24	CEBPB	chr4:100009224-100009596	A549	lung:	n/a	chr4:100009401-100009412 chr4:100009400-100009413
25	CHD2	chr4:100009156-100010218	Hela-S3	cervix:	n/a	n/a
26	YY1	chr4:100009456-100010257	SK-N-SH	brain:	n/a	chr4:100009843-100009855
27	SIN3AK20	chr4:100009360-100010523	MCF-7	breast:	n/a	n/a
28	STAT3	chr4:100009325-100009605	MCF10A-Er-Src	breast:	n/a	chr4:100009588-100009600
29	MXI1	chr4:100009161-100010651	GM12878	blood:	n/a	n/a
30	CEBPB	chr4:100009196-100009590	ECC-1	luminal epithelium:	n/a	chr4:100009401-100009412 chr4:100009400-100009413
31	USF2	chr4:100009566-100009696	H1-hESC	embryonic stem cell:	n/a	n/a
32	SP1	chr4:100009546-100010551	A549	lung:	n/a	chr4:100009567-100009581 chr4:100009590-100009604
33	POLR2A	chr4:100009500-100010417	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr4:100009584-100010405	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr4:100009386-100011182	K562	blood:	n/a	n/a
36	POLR2A	chr4:100009589-100010262	A549	lung:	n/a	n/a
37	ATF2	chr4:100009560-100010260	GM12878	blood:	n/a	n/a
38	MYC	chr4:100009292-100011454	K562	blood:	n/a	n/a
39	POLR2A	chr4:100008635-100010677	K562	blood:	n/a	n/a
40	POLR2A	chr4:100009517-100010344	GM12878	blood:	n/a	n/a
41	MYBL2	chr4:100009581-100010473	HepG2	liver:	n/a	n/a
42	IRF1	chr4:100008475-100010640	K562	blood:	n/a	n/a
43	TAF1	chr4:100009572-100010223	HepG2	liver:	n/a	n/a
44	BHLHE40	chr4:100009166-100011411	K562	blood:	n/a	n/a
45	TAF1	chr4:100009580-100010276	MCF-7	breast:	n/a	n/a
46	POLR2A	chr4:100009378-100010454	GM18505	blood:	n/a	n/a
47	POLR2A	chr4:100009493-100010659	K562	blood:	n/a	n/a
48	POLR2A	chr4:100009334-100010320	Hela-S3	cervix:	n/a	n/a
49	MAX	chr4:100009324-100010480	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr4:100009483-100010548	U87	brain:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:100008381..100011330-chr4:100056699..100058939,2	MCF-7	breast:
2	chr4:99987489..99989654-chr4:100009071..100011507,2	MCF-7	breast:
3	chr4:99914937..99918533-chr4:100007922..100010203,4	K562	blood:
4	chr12:7052144..7053435-chr4:100009518..100010498,3	Hela-S3	cervix:
5	chr4:99951373..99953005-chr4:100007401..100010388,2	MCF-7	breast:
6	chr4:99915265..99918330-chr4:100008518..100010769,3	K562	blood:
7	chr4:99915764..99917972-chr4:100008352..100010409,2	MCF-7	breast:
8	chr22:24236720..24237273-chr4:100009330..100009909,2	NB4	blood:
9	chr4:100009539..100010373-chrX:41193722..41194435,2	Hela-S3	cervix:
10	chr16:31191097..31191842-chr4:100009488..100010016,2	Hela-S3	cervix:
11	chr4:99915328..99918402-chr4:100008331..100011431,5	MCF-7	breast:
12	chr4:100008800..100012914-chr4:100866380..100869813,4	K562	blood:
13	chr4:99849612..99852371-chr4:100007085..100010224,5	K562	blood:
14	chr4:99848192..99852255-chr4:100007586..100012546,7	K562	blood:
15	chr11:65189876..65190596-chr4:100009207..100010180,2	HCT-116	colon:
16	chr4:99849574..99853806-chr4:100008192..100011466,4	MCF-7	breast:
17	chr4:100008800..100013313-chr4:100866380..100869813,5	K562	blood:
18	chr4:100009534..100010241-chr4:100870932..100871664,2	NB4	blood:

No data

Variant related genes	Relation type
ENSG00000246090	TF binding region
ADH5	TF binding region
ENSG00000164031	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000238923	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000198099	Chromatin interaction
ENSG00000240972	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000272777	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000215301	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000263923	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1154400	0.94[EUR][1000 genomes]
rs1154401	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1154405	0.80[EUR][1000 genomes]
rs1154406	0.80[EUR][1000 genomes]
rs1230155	0.86[AMR][1000 genomes]
rs1230158	0.86[AMR][1000 genomes]
rs12502237	0.93[EUR][1000 genomes]
rs1311620	0.93[EUR][1000 genomes]
rs13832	0.87[AMR][1000 genomes]
rs1453872	0.91[EUR][1000 genomes]
rs1840229	0.89[EUR][1000 genomes]
rs1901922	0.91[EUR][1000 genomes]
rs2602840	0.92[EUR][1000 genomes]
rs2602851	0.91[EUR][1000 genomes]
rs2602853	0.91[EUR][1000 genomes]
rs2602854	0.91[EUR][1000 genomes]
rs2602856	0.83[AMR][1000 genomes]
rs2602857	0.91[EUR][1000 genomes]
rs2602860	0.82[EUR][1000 genomes]
rs2602862	0.82[EUR][1000 genomes]
rs2602875	0.80[EUR][1000 genomes]
rs2851259	0.82[EUR][1000 genomes]
rs2851270	0.86[AMR][1000 genomes]
rs2851274	0.89[AMR][1000 genomes]
rs2851279	0.90[EUR][1000 genomes]
rs2851284	0.91[EUR][1000 genomes]
rs3018046	0.91[EUR][1000 genomes]
rs3100630	0.90[EUR][1000 genomes]
rs3133152	0.90[EUR][1000 genomes]
rs4235435	0.81[EUR][1000 genomes]
rs6831257	0.91[AMR][1000 genomes]
rs896992	0.87[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1154403	ADH5	cis	brain	BrainEAC
rs1154403	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100006600-100011400	Active TSS	Colonic Mucosa	Colon
2	chr4:100006600-100012400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:100006800-100012400	Active TSS	NHLF	lung
4	chr4:100007000-100009600	Active TSS	Aorta	Aorta
5	chr4:100007000-100011600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:100007000-100011600	Active TSS	Duodenum Mucosa	Duodenum
7	chr4:100007200-100010800	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr4:100007200-100011000	Active TSS	Fetal Intestine Small	intestine
9	chr4:100007400-100012400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr4:100007400-100012600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:100007600-100011800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:100007600-100012200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr4:100007800-100010200	Active TSS	Liver	Liver
14	chr4:100007800-100010800	Active TSS	Hela-S3	cervix
15	chr4:100007800-100011000	Active TSS	A549	lung
16	chr4:100007800-100011200	Active TSS	Muscle Satellite Cultured Cells	--
17	chr4:100007800-100012200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:100007800-100013400	Active TSS	K562	blood
19	chr4:100008000-100012400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:100008200-100010200	Active TSS	Placenta	Placenta
21	chr4:100008200-100011000	Active TSS	HSMM	muscle
22	chr4:100008200-100011400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr4:100008200-100011400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr4:100008200-100011400	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr4:100008200-100011600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:100008200-100011600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:100008400-100009600	Active TSS	Right Atrium	heart
28	chr4:100008400-100010800	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr4:100008400-100011000	Active TSS	H1 Cell Line	embryonic stem cell
30	chr4:100008400-100011000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:100008400-100011200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:100008400-100011200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:100008400-100011200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:100008400-100011600	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr4:100008400-100011600	Active TSS	NHDF-Ad	bronchial
36	chr4:100008400-100011800	Active TSS	NHEK	skin
37	chr4:100008400-100012200	Active TSS	Brain Germinal Matrix	brain
38	chr4:100008400-100012400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:100008400-100012400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:100008600-100009600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:100008600-100010800	Active TSS	Brain Cingulate Gyrus	brain
42	chr4:100008600-100010800	Active TSS	Pancreas	Pancrea
43	chr4:100008600-100010800	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr4:100008600-100010800	Active TSS	Thymus	Thymus
45	chr4:100008600-100010800	Active TSS	HUVEC	blood vessel
46	chr4:100008600-100011000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:100008600-100011000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:100008600-100011000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:100008600-100011000	Active TSS	Fetal Intestine Large	intestine
50	chr4:100008600-100011400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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