Variant report

Variant	rs29001338
Chromosome Location	chr4:100011250-100011251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MEF2A	chr4:100010869-100011377	K562	blood:	n/a	chr4:100010940-100010961 chr4:100011087-100011102 chr4:100010947-100010958
2	POLR2A	chr4:100010810-100011450	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA3	chr4:100011029-100011355	SH-SY5Y	brain:	n/a	n/a
4	TBL1XR1	chr4:100011032-100011460	K562	blood:	n/a	n/a
5	ARID3A	chr4:100011229-100011288	HepG2	liver:	n/a	n/a
6	MYC	chr4:100009292-100011454	K562	blood:	n/a	n/a
7	BHLHE40	chr4:100009166-100011411	K562	blood:	n/a	n/a
8	GATA2	chr4:100010594-100011289	SH-SY5Y	brain:	n/a	n/a
9	ZNF143	chr4:100011100-100011300	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr4:100008557-100011869	IMR90	lung:	n/a	n/a
11	UBTF	chr4:100011019-100011420	K562	blood:	n/a	n/a
12	TBP	chr4:100010738-100011399	K562	blood:	n/a	n/a
13	UBTF	chr4:100011152-100011490	K562	blood:	n/a	n/a
14	POLR2A	chr4:100009092-100011459	K562	blood:	n/a	n/a
15	HEY1	chr4:100009494-100011541	K562	blood:	n/a	n/a
16	POLR2A	chr4:100009268-100011370	K562	blood:	n/a	n/a
17	JUND	chr4:100010853-100011309	K562	blood:	n/a	n/a
18	MAX	chr4:100011166-100011271	HepG2	liver:	n/a	n/a
19	STAT3	chr4:100010788-100011322	MCF10A-Er-Src	breast:	n/a	n/a
20	HEY1	chr4:100010877-100011431	HepG2	liver:	n/a	n/a
21	ZNF143	chr4:100011167-100011444	K562	blood:	n/a	n/a
22	CCNT2	chr4:100010974-100011296	K562	blood:	n/a	n/a
23	MEF2A	chr4:100010878-100011276	K562	blood:	n/a	chr4:100010940-100010961 chr4:100011087-100011102 chr4:100010947-100010958
24	STAT3	chr4:100010797-100011297	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr4:100010636-100011453	K562	blood:	n/a	n/a
26	RCOR1	chr4:100010909-100011468	K562	blood:	n/a	n/a
27	EP300	chr4:100010895-100011392	K562	blood:	n/a	n/a
28	ZMIZ1	chr4:100011021-100011424	K562	blood:	n/a	n/a
29	RCOR1	chr4:100011084-100011438	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:100008381..100011330-chr4:100056699..100058939,2	MCF-7	breast:
2	chr4:99955536..99957055-chr4:100010118..100011890,2	K562	blood:
3	chr4:100010805..100012670-chr4:100870311..100872681,2	K562	blood:
4	chr4:99987489..99989654-chr4:100009071..100011507,2	MCF-7	breast:
5	chr4:100010072..100012637-chr4:100483853..100485997,3	K562	blood:
6	chr4:99915328..99918402-chr4:100008331..100011431,5	MCF-7	breast:
7	chr4:100010297..100012013-chr4:100018638..100021523,2	K562	blood:
8	chr4:100010287..100011807-chr4:100330778..100333619,2	MCF-7	breast:
9	chr4:100008800..100012914-chr4:100866380..100869813,4	K562	blood:
10	chr4:99848192..99852255-chr4:100007586..100012546,7	K562	blood:
11	chr4:99849574..99853806-chr4:100008192..100011466,4	MCF-7	breast:
12	chr4:100008800..100013313-chr4:100866380..100869813,5	K562	blood:

No data

Variant related genes	Relation type
ADH5	TF binding region
ENSG00000198099	Chromatin interaction
ENSG00000145331	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000272777	Chromatin interaction
ENSG00000263923	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000164031	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000138823	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10002449	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10084896	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17028370	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17028770	0.83[AMR][1000 genomes]
rs2018417	0.83[AMR][1000 genomes]
rs28364314	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28720156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28730581	1.00[EUR][1000 genomes]
rs28730584	1.00[EUR][1000 genomes]
rs28730596	1.00[EUR][1000 genomes]
rs28730601	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28730611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730617	1.00[EUR][1000 genomes]
rs28730625	1.00[EUR][1000 genomes]
rs28730641	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730643	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730644	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730645	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730649	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28894370	1.00[EUR][1000 genomes]
rs28894371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28914786	0.83[AMR][1000 genomes]
rs29001228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs29001342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001346	1.00[EUR][1000 genomes]
rs29001348	1.00[EUR][1000 genomes]
rs4499706	0.92[EUR][1000 genomes]
rs5003497	1.00[EUR][1000 genomes]
rs55831712	0.81[EUR][1000 genomes]
rs55963727	0.83[AMR][1000 genomes]
rs61431883	1.00[EUR][1000 genomes]
rs62323213	0.81[EUR][1000 genomes]
rs62323214	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62323216	0.81[EUR][1000 genomes]
rs62323217	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62323230	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323231	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323233	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323234	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323235	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323236	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323237	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323238	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323242	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323244	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323245	1.00[AMR][1000 genomes]
rs62323246	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323247	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323248	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323249	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323250	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323251	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323252	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323253	0.81[EUR][1000 genomes]
rs62323254	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323256	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323258	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62323259	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325160	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325161	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325182	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325183	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325184	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325185	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325186	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325187	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325188	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325189	0.81[EUR][1000 genomes]
rs62325190	0.83[AMR][1000 genomes]
rs62325192	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325193	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325194	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325195	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325196	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325197	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325198	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325199	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325200	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325201	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325202	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325203	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325204	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325205	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325206	0.81[EUR][1000 genomes]
rs62325208	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325209	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325210	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325211	0.81[EUR][1000 genomes]
rs62325212	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325213	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325236	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325237	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325238	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325240	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325241	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325242	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532781	1.00[EUR][1000 genomes]
rs6532792	1.00[EUR][1000 genomes]
rs6819694	1.00[EUR][1000 genomes]
rs6819724	1.00[EUR][1000 genomes]
rs6822742	1.00[EUR][1000 genomes]
rs6823388	1.00[EUR][1000 genomes]
rs6827292	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72897156	1.00[EUR][1000 genomes]
rs72897165	0.92[EUR][1000 genomes]
rs72897167	0.92[EUR][1000 genomes]
rs7667261	1.00[EUR][1000 genomes]
rs7679102	1.00[EUR][1000 genomes]
rs7681427	1.00[EUR][1000 genomes]
rs7687322	1.00[EUR][1000 genomes]
rs7688859	0.93[EUR][1000 genomes]
rs7699232	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9995869	0.81[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
rs29001338	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 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	chr4:100007000-100011600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:100007000-100011600	Active TSS	Duodenum Mucosa	Duodenum
6	chr4:100007400-100012400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr4:100007400-100012600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr4:100007600-100011800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr4:100007600-100012200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr4:100007800-100012200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:100007800-100013400	Active TSS	K562	blood
12	chr4:100008000-100012400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:100008200-100011400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr4:100008200-100011400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr4:100008200-100011400	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr4:100008200-100011600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:100008200-100011600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:100008400-100011600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr4:100008400-100011600	Active TSS	NHDF-Ad	bronchial
20	chr4:100008400-100011800	Active TSS	NHEK	skin
21	chr4:100008400-100012200	Active TSS	Brain Germinal Matrix	brain
22	chr4:100008400-100012400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:100008400-100012400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:100008600-100011400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:100008600-100011400	Active TSS	Fetal Kidney	kidney
26	chr4:100008600-100011400	Active TSS	GM12878-XiMat	blood
27	chr4:100008600-100011800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:100008600-100012000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:100008600-100012200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr4:100008600-100012200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:100008600-100012800	Active TSS	Ovary	ovary
32	chr4:100008800-100011400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:100008800-100011400	Active TSS	Psoas Muscle	Psoas
34	chr4:100008800-100011600	Active TSS	HMEC	breast
35	chr4:100009000-100011400	Active TSS	Esophagus	oesophagus
36	chr4:100009000-100011600	Active TSS	HSMMtube	muscle
37	chr4:100009000-100011800	Active TSS	Rectal Smooth Muscle	rectum
38	chr4:100009200-100011400	Active TSS	Brain Substantia Nigra	brain
39	chr4:100009200-100011400	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr4:100009400-100012000	Active TSS	Fetal Brain Female	brain
41	chr4:100009400-100012000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr4:100009400-100012800	Active TSS	Stomach Smooth Muscle	stomach
43	chr4:100010000-100011400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr4:100010000-100012400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:100010000-100012400	Active TSS	Aorta	Aorta
46	chr4:100010200-100011400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:100010200-100011400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:100010200-100011400	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr4:100010200-100011400	Flanking Active TSS	Liver	Liver
50	chr4:100010200-100011400	Active TSS	Right Atrium	heart

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