Variant report

Variant	rs62325189
Chromosome Location	chr4:99952696-99952697
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99951373..99953005-chr4:100007401..100010388,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197894	Chromatin interaction
ENSG00000246090	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10002449	1.00[EUR][1000 genomes]
rs10084896	1.00[EUR][1000 genomes]
rs17028370	1.00[EUR][1000 genomes]
rs28659806	0.96[EUR][1000 genomes]
rs28730581	0.81[EUR][1000 genomes]
rs28730584	0.81[EUR][1000 genomes]
rs28730596	0.81[EUR][1000 genomes]
rs28730611	0.81[EUR][1000 genomes]
rs28730617	0.81[EUR][1000 genomes]
rs28730625	0.81[EUR][1000 genomes]
rs28730641	0.81[EUR][1000 genomes]
rs28730643	0.81[EUR][1000 genomes]
rs28730644	0.81[EUR][1000 genomes]
rs28730645	0.81[EUR][1000 genomes]
rs28730646	0.81[EUR][1000 genomes]
rs28730649	0.81[EUR][1000 genomes]
rs28894370	0.81[EUR][1000 genomes]
rs29001338	0.81[EUR][1000 genomes]
rs29001342	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	1.00[EUR][1000 genomes]
rs62323231	1.00[EUR][1000 genomes]
rs62323233	1.00[EUR][1000 genomes]
rs62323234	1.00[EUR][1000 genomes]
rs62323235	1.00[EUR][1000 genomes]
rs62323236	1.00[EUR][1000 genomes]
rs62323237	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62323238	1.00[EUR][1000 genomes]
rs62323240	1.00[EUR][1000 genomes]
rs62323241	1.00[EUR][1000 genomes]
rs62323242	1.00[EUR][1000 genomes]
rs62323244	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62323245	0.92[EUR][1000 genomes]
rs62323246	1.00[EUR][1000 genomes]
rs62323247	1.00[EUR][1000 genomes]
rs62323248	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62323249	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62323250	1.00[EUR][1000 genomes]
rs62323251	1.00[EUR][1000 genomes]
rs62323252	1.00[EUR][1000 genomes]
rs62323253	1.00[EUR][1000 genomes]
rs62323254	1.00[EUR][1000 genomes]
rs62323255	1.00[EUR][1000 genomes]
rs62323256	1.00[EUR][1000 genomes]
rs62323257	1.00[EUR][1000 genomes]
rs62323258	1.00[EUR][1000 genomes]
rs62323259	1.00[EUR][1000 genomes]
rs62325160	1.00[EUR][1000 genomes]
rs62325161	1.00[EUR][1000 genomes]
rs62325182	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325183	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325184	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325185	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325186	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325187	1.00[EUR][1000 genomes]
rs62325188	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325190	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62325192	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325193	1.00[EUR][1000 genomes]
rs62325194	1.00[EUR][1000 genomes]
rs62325195	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325196	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325197	1.00[EUR][1000 genomes]
rs62325198	1.00[EUR][1000 genomes]
rs62325199	1.00[EUR][1000 genomes]
rs62325200	1.00[EUR][1000 genomes]
rs62325201	1.00[EUR][1000 genomes]
rs62325202	1.00[EUR][1000 genomes]
rs62325203	1.00[EUR][1000 genomes]
rs62325204	1.00[EUR][1000 genomes]
rs62325205	1.00[EUR][1000 genomes]
rs62325206	1.00[EUR][1000 genomes]
rs62325208	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325209	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325210	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325211	1.00[EUR][1000 genomes]
rs62325212	1.00[EUR][1000 genomes]
rs62325213	1.00[EUR][1000 genomes]
rs62325236	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325237	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325238	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325239	0.81[EUR][1000 genomes]
rs62325240	0.81[EUR][1000 genomes]
rs62325241	0.81[EUR][1000 genomes]
rs62325242	0.81[EUR][1000 genomes]
rs62325245	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	0.81[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]
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
rs62325189	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99931600-99971400	Weak transcription	Aorta	Aorta
2	chr4:99932600-99969800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:99937600-99966200	Weak transcription	HUVEC	blood vessel
4	chr4:99942200-99969600	Weak transcription	Fetal Brain Female	brain
5	chr4:99942600-99953400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:99942800-99955800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:99942800-99957000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:99943000-99959200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:99943600-99953400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:99943800-99966200	Weak transcription	Adipose Nuclei	Adipose
11	chr4:99944200-99966200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:99944200-99968800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:99944200-99969600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:99944200-99979000	Weak transcription	Colonic Mucosa	Colon
15	chr4:99944200-99979200	Weak transcription	Right Ventricle	heart
16	chr4:99944400-99952800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:99944400-99955200	Weak transcription	NH-A	brain
18	chr4:99944400-99955400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr4:99944400-99958400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:99944400-99958800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:99944400-99958800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:99944400-99958800	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:99944400-99959400	Weak transcription	HSMM	muscle
24	chr4:99944400-99965000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:99944400-99966400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:99944400-99967200	Weak transcription	Fetal Stomach	stomach
27	chr4:99944400-99971600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:99944400-99979200	Weak transcription	Brain Hippocampus Middle	brain
29	chr4:99945000-99969600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:99945600-99957000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:99946000-99976800	Weak transcription	Stomach Mucosa	stomach
32	chr4:99946200-99953600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:99946200-99970000	Weak transcription	Brain Anterior Caudate	brain
34	chr4:99946200-99977000	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:99946400-99969000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:99946400-99969400	Weak transcription	Placenta	Placenta
37	chr4:99946400-99973600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:99946400-99979000	Weak transcription	Esophagus	oesophagus
39	chr4:99946600-99964800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr4:99946600-99970000	Weak transcription	Hela-S3	cervix
41	chr4:99947000-99953200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr4:99947000-99955200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:99947000-99955600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:99947000-99957200	Weak transcription	Fetal Lung	lung
45	chr4:99947000-99964800	Weak transcription	Left Ventricle	heart
46	chr4:99947000-99969600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:99947000-99969800	Weak transcription	Ovary	ovary
48	chr4:99947000-99979000	Weak transcription	Gastric	stomach
49	chr4:99947000-99979200	Weak transcription	Pancreas	Pancrea
50	chr4:99947200-99955200	Weak transcription	Rectal Mucosa Donor 31	rectum

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