Variant report

Variant	rs28730584
Chromosome Location	chr4:100005204-100005205
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	POLR2A	chr4:100004731-100006168	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:100005035-100006268	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:100004956-100005712	K562	blood:	n/a	n/a
4	POLR2A	chr4:100005190-100005641	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:100004875-100005444	HepG2	liver:	n/a	n/a
6	HEY1	chr4:100005178-100005927	HepG2	liver:	n/a	chr4:100005187-100005196
7	POLR2A	chr4:100004027-100005209	HepG2	liver:	n/a	n/a
8	POLR2A	chr4:100005068-100005609	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr4:100004973-100005341	K562	blood:	n/a	n/a
10	POLR2A	chr4:100005089-100005653	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:100004049-100006136	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99916814..99918708-chr4:100004523..100006516,2	MCF-7	breast:

Variant related genes	Relation type
ADH5	TF binding region
ENSG00000246090	TF binding region
ENSG00000265213	Chromatin interaction
ENSG00000164024	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10002449	0.81[EUR][1000 genomes]
rs10084896	0.81[EUR][1000 genomes]
rs17028370	0.81[EUR][1000 genomes]
rs28730581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730596	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730601	0.96[EUR][1000 genomes]
rs28730611	1.00[EUR][1000 genomes]
rs28730617	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730625	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730641	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730643	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730644	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730645	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28730646	1.00[EUR][1000 genomes]
rs28730649	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28894370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28894371	0.87[EUR][1000 genomes]
rs29001338	1.00[EUR][1000 genomes]
rs29001342	1.00[EUR][1000 genomes]
rs29001346	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001348	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4295271	0.85[AMR][1000 genomes]
rs4499706	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5003497	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55831712	0.81[EUR][1000 genomes]
rs61431883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323213	0.81[EUR][1000 genomes]
rs62323214	0.81[EUR][1000 genomes]
rs62323216	0.81[EUR][1000 genomes]
rs62323217	0.81[EUR][1000 genomes]
rs62323230	0.81[EUR][1000 genomes]
rs62323231	0.81[EUR][1000 genomes]
rs62323233	0.81[EUR][1000 genomes]
rs62323234	0.81[EUR][1000 genomes]
rs62323235	0.81[EUR][1000 genomes]
rs62323236	0.81[EUR][1000 genomes]
rs62323237	0.81[EUR][1000 genomes]
rs62323238	0.81[EUR][1000 genomes]
rs62323240	0.81[EUR][1000 genomes]
rs62323241	0.81[EUR][1000 genomes]
rs62323242	0.81[EUR][1000 genomes]
rs62323244	0.81[EUR][1000 genomes]
rs62323246	0.81[EUR][1000 genomes]
rs62323247	0.81[EUR][1000 genomes]
rs62323248	0.81[EUR][1000 genomes]
rs62323249	0.81[EUR][1000 genomes]
rs62323250	0.81[EUR][1000 genomes]
rs62323251	0.81[EUR][1000 genomes]
rs62323252	0.81[EUR][1000 genomes]
rs62323253	0.81[EUR][1000 genomes]
rs62323254	0.81[EUR][1000 genomes]
rs62323255	0.81[EUR][1000 genomes]
rs62323256	0.81[EUR][1000 genomes]
rs62323257	0.81[EUR][1000 genomes]
rs62323258	0.81[EUR][1000 genomes]
rs62323259	0.81[EUR][1000 genomes]
rs62325160	0.81[EUR][1000 genomes]
rs62325161	0.81[EUR][1000 genomes]
rs62325182	0.81[EUR][1000 genomes]
rs62325183	0.81[EUR][1000 genomes]
rs62325184	0.81[EUR][1000 genomes]
rs62325185	0.81[EUR][1000 genomes]
rs62325186	0.81[EUR][1000 genomes]
rs62325187	0.81[EUR][1000 genomes]
rs62325188	0.81[EUR][1000 genomes]
rs62325189	0.81[EUR][1000 genomes]
rs62325192	0.81[EUR][1000 genomes]
rs62325193	0.81[EUR][1000 genomes]
rs62325194	0.81[EUR][1000 genomes]
rs62325195	0.81[EUR][1000 genomes]
rs62325196	0.81[EUR][1000 genomes]
rs62325197	0.81[EUR][1000 genomes]
rs62325198	0.81[EUR][1000 genomes]
rs62325199	0.81[EUR][1000 genomes]
rs62325200	0.81[EUR][1000 genomes]
rs62325201	0.81[EUR][1000 genomes]
rs62325202	0.81[EUR][1000 genomes]
rs62325203	0.81[EUR][1000 genomes]
rs62325204	0.81[EUR][1000 genomes]
rs62325205	0.81[EUR][1000 genomes]
rs62325206	0.81[EUR][1000 genomes]
rs62325208	0.81[EUR][1000 genomes]
rs62325209	0.81[EUR][1000 genomes]
rs62325210	0.81[EUR][1000 genomes]
rs62325211	0.81[EUR][1000 genomes]
rs62325212	0.81[EUR][1000 genomes]
rs62325213	0.81[EUR][1000 genomes]
rs62325236	0.81[EUR][1000 genomes]
rs62325237	0.81[EUR][1000 genomes]
rs62325238	0.81[EUR][1000 genomes]
rs62325239	1.00[EUR][1000 genomes]
rs62325240	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325241	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325242	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325245	1.00[EUR][1000 genomes]
rs6532781	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6532792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6819694	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6819724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6822742	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6823388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6827292	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72897156	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72897165	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72897167	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7667261	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7679102	1.00[EUR][1000 genomes]
rs7681427	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7687322	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7688859	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7699232	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9995869	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28730584	ADH5	Cis_1M	lymphoblastoid	RTeQTL

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	chr4:99978000-100007800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:99983200-100008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:99985600-100006600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:99987200-100005400	Strong transcription	Dnd41	blood
7	chr4:99987200-100006600	Strong transcription	HSMM	muscle
8	chr4:99987200-100008000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:99987400-100007600	Strong transcription	Fetal Thymus	thymus
10	chr4:99987600-100006000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:99987600-100006600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:99987800-100006800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:99987800-100007000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:99988000-100006800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:99988000-100007000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:99988200-100006400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:99988400-100007000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:99989000-100006600	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr4:99989000-100006800	Strong transcription	Primary T cells from cord blood	blood
20	chr4:99989400-100007400	Strong transcription	HMEC	breast
21	chr4:99989600-100007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:99990400-100005600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:99990400-100006400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:99990600-100007200	Strong transcription	Osteobl	bone
25	chr4:99990600-100007400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:99990800-100007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:99991000-100006200	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr4:99991200-100006000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:99991200-100006800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr4:99991200-100007000	Strong transcription	Primary B cells from cord blood	blood
31	chr4:99991200-100007400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr4:99991200-100007400	Strong transcription	NHDF-Ad	bronchial
33	chr4:99991400-100006600	Strong transcription	Fetal Intestine Large	intestine
34	chr4:99991400-100006800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr4:99991400-100006800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr4:99991400-100007000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:99991400-100007000	Strong transcription	Thymus	Thymus
38	chr4:99991400-100007000	Strong transcription	HUVEC	blood vessel
39	chr4:99991400-100007400	Strong transcription	Fetal Lung	lung
40	chr4:99991600-100006600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:99991600-100006800	Strong transcription	K562	blood
42	chr4:99991600-100007000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:99992400-100006400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr4:99992400-100007200	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr4:99992400-100007200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:99992400-100007200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:99992600-100007000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr4:99992800-100006800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:99993000-100005400	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr4:99994200-100006200	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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