Variant report

Variant	rs62325204
Chromosome Location	chr4:99971901-99971902
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99921481..99924289-chr4:99969597..99972369,2	K562	blood:
2	chr4:99969379..99972203-chr4:99982602..99986202,3	K562	blood:
3	chr4:99916028..99916613-chr4:99971612..99972143,2	MCF-7	breast:
4	chr4:99970407..99973729-chr4:99975886..99978831,3	K562	blood:
5	chr4:99915986..99917562-chr4:99970036..99972907,2	K562	blood:

Variant related genes	Relation type
ENSG00000164024	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

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]
rs17028770	0.83[AMR][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]
rs62323254	1.00[AMR][1000 genomes];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[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]
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:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62325204	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99944200-99979000	Weak transcription	Colonic Mucosa	Colon
2	chr4:99944200-99979200	Weak transcription	Right Ventricle	heart
3	chr4:99944400-99979200	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:99946000-99976800	Weak transcription	Stomach Mucosa	stomach
5	chr4:99946200-99977000	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:99946400-99973600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:99946400-99979000	Weak transcription	Esophagus	oesophagus
8	chr4:99947000-99979000	Weak transcription	Gastric	stomach
9	chr4:99947000-99979200	Weak transcription	Pancreas	Pancrea
10	chr4:99947400-99982600	Weak transcription	Psoas Muscle	Psoas
11	chr4:99949000-99979000	Weak transcription	Small Intestine	intestine
12	chr4:99949600-99973200	Weak transcription	Fetal Kidney	kidney
13	chr4:99954000-99999200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:99954600-99976600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:99954800-99977000	Weak transcription	Brain Substantia Nigra	brain
16	chr4:99955400-99980800	Weak transcription	HSMMtube	muscle
17	chr4:99956200-99995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:99959400-99976200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:99959600-99976000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:99959800-99973600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:99959800-100000200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:99960400-99973400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:99961600-99976200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:99964000-99976600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:99964200-99976200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:99964200-99979000	Weak transcription	Brain Germinal Matrix	brain
27	chr4:99964400-99976400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:99965000-99982000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:99965000-99982200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:99965200-99972600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:99965600-99976800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:99965600-99976800	Strong transcription	Fetal Thymus	thymus
33	chr4:99965600-99977000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:99965600-99977200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:99965800-99974400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:99965800-99974800	Strong transcription	Primary B cells from cord blood	blood
37	chr4:99966000-99976200	Strong transcription	Primary T cells from cord blood	blood
38	chr4:99966200-99972200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:99966200-99976200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:99966400-99972400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:99966400-99973800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr4:99966600-99977000	Weak transcription	HUVEC	blood vessel
43	chr4:99966800-99973600	Weak transcription	NHDF-Ad	bronchial
44	chr4:99967000-99974800	Strong transcription	Fetal Intestine Large	intestine
45	chr4:99967200-99972600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:99968000-99972000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:99968200-99976000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:99968200-99976000	Strong transcription	Dnd41	blood
49	chr4:99968400-99974000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:99968600-99977000	Weak transcription	Brain Angular Gyrus	brain

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