Variant report

Variant	rs62323254
Chromosome Location	chr4:99937251-99937252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99936895..99940031-chr4:99942531..99946940,4	K562	blood:
2	chr4:99936357..99938294-chr4:99938962..99941752,2	K562	blood:
3	chr4:99928910..99931471-chr4:99936382..99940065,3	K562	blood:
4	chr4:99936341..99939082-chr4:99948157..99950899,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164024	Chromatin interaction
ENSG00000250496	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10002449	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10084896	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17028370	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28659806	0.96[EUR][1000 genomes]
rs28720156	1.00[AMR][1000 genomes]
rs28730581	0.81[EUR][1000 genomes]
rs28730584	0.81[EUR][1000 genomes]
rs28730596	0.81[EUR][1000 genomes]
rs28730601	0.83[AMR][1000 genomes]
rs28730611	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28730617	0.81[EUR][1000 genomes]
rs28730625	0.81[EUR][1000 genomes]
rs28730641	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28730643	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28730644	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28730645	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28730646	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28730649	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28894370	0.81[EUR][1000 genomes]
rs28894371	1.00[AMR][1000 genomes]
rs29001228	1.00[AMR][1000 genomes]
rs29001338	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs29001342	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs29001346	0.81[EUR][1000 genomes]
rs29001348	0.81[EUR][1000 genomes]
rs5003497	0.81[EUR][1000 genomes]
rs55831712	1.00[EUR][1000 genomes]
rs61431883	0.81[EUR][1000 genomes]
rs62323213	1.00[EUR][1000 genomes]
rs62323214	1.00[EUR][1000 genomes]
rs62323216	1.00[EUR][1000 genomes]
rs62323217	1.00[EUR][1000 genomes]
rs62323230	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323231	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323233	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323234	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323235	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323236	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323237	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323238	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323241	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323244	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323245	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62323246	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323247	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323248	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323249	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323251	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323252	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323253	1.00[EUR][1000 genomes]
rs62323255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323256	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323257	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323259	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325160	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325161	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325182	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325183	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325184	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325185	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325186	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325187	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325188	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325189	1.00[EUR][1000 genomes]
rs62325190	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62325192	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325193	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325194	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325195	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325196	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325197	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325198	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325199	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325200	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325202	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325203	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325205	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325206	1.00[EUR][1000 genomes]
rs62325208	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325209	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325210	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325211	1.00[EUR][1000 genomes]
rs62325212	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325236	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325237	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325238	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325239	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325240	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325241	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325242	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325245	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6532781	0.81[EUR][1000 genomes]
rs6532792	0.81[EUR][1000 genomes]
rs6819694	0.81[EUR][1000 genomes]
rs6819724	0.81[EUR][1000 genomes]
rs6822742	0.81[EUR][1000 genomes]
rs6823388	0.81[EUR][1000 genomes]
rs6827292	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72897156	0.81[EUR][1000 genomes]
rs7667261	0.81[EUR][1000 genomes]
rs7679102	0.81[EUR][1000 genomes]
rs7681427	0.81[EUR][1000 genomes]
rs7687322	0.81[EUR][1000 genomes]
rs7699232	0.83[AMR][1000 genomes]
rs9995869	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62323254	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99918200-99938000	Weak transcription	NHDF-Ad	bronchial
2	chr4:99918600-99937800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:99918600-99938600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:99918800-99937800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:99919200-99940000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:99919200-99942000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:99920000-99937800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:99924200-99941600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:99924200-99943600	Weak transcription	Gastric	stomach
10	chr4:99924600-99942000	Weak transcription	Fetal Lung	lung
11	chr4:99925400-99940000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:99925600-99939800	Weak transcription	Thymus	Thymus
13	chr4:99925600-99941200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:99925600-99941200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:99925800-99938800	Weak transcription	Fetal Intestine Large	intestine
16	chr4:99928400-99941400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:99928600-99942400	Weak transcription	Esophagus	oesophagus
18	chr4:99929200-99940600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:99929200-99940800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:99930200-99938000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr4:99930600-99941400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr4:99930600-99941400	Weak transcription	NHEK	skin
23	chr4:99931600-99971400	Weak transcription	Aorta	Aorta
24	chr4:99931800-99940600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:99932000-99940200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:99932400-99937400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:99932600-99937800	Weak transcription	Dnd41	blood
28	chr4:99932600-99969800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr4:99933600-99938200	Weak transcription	Fetal Thymus	thymus
30	chr4:99934000-99938600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:99934000-99941600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:99934200-99941600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:99934600-99941200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:99934800-99944800	Weak transcription	Small Intestine	intestine
35	chr4:99935000-99938800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:99935000-99941000	Weak transcription	HMEC	breast
37	chr4:99935000-99945400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:99935400-99938800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:99935400-99940800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr4:99935400-99941400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:99935400-99941600	Weak transcription	HepG2	liver
42	chr4:99935400-99945600	Weak transcription	Colon Smooth Muscle	Colon
43	chr4:99935600-99940000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr4:99935600-99940400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr4:99935600-99941800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr4:99935600-99944400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr4:99935800-99937400	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr4:99935800-99938000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:99935800-99941600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:99936200-99938000	Weak transcription	Spleen	Spleen

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