Variant report

Variant	rs62325184
Chromosome Location	chr4:99943836-99943837
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	CBX3	chr4:99943800-99944135	K562	blood:	n/a	n/a
2	TRIM28	chr4:99943731-99944219	K562	blood:	n/a	n/a
3	POLR2A	chr4:99943774-99944352	K562	blood:	n/a	n/a
4	CBX3	chr4:99943729-99944303	K562	blood:	n/a	n/a
5	SETDB1	chr4:99943820-99944207	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:99942650..99945674-chr6:26595832..26598932,6	K562	blood:
2	chr4:99942655..99945658-chr6:26596311..26598592,3	MCF-7	breast:
3	chr4:99915525..99918321-chr4:99942451..99944575,2	K562	blood:

Variant related genes	Relation type
METAP1	TF binding region
ENSG00000146109	Chromatin interaction
ENSG00000164024	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10002449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10084896	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17028370	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28659806	0.96[EUR][1000 genomes]
rs28720156	0.83[AMR][1000 genomes]
rs28730581	0.81[EUR][1000 genomes]
rs28730584	0.81[EUR][1000 genomes]
rs28730596	0.81[EUR][1000 genomes]
rs28730611	0.83[AMR][1000 genomes];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	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28730649	0.81[EUR][1000 genomes]
rs28894370	0.81[EUR][1000 genomes]
rs28894371	0.83[AMR][1000 genomes]
rs29001228	0.83[AMR][1000 genomes]
rs29001338	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs29001342	0.83[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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323231	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323233	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323234	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323235	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323236	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323240	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323241	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323242	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323245	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62323246	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323247	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323250	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323251	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323252	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323253	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323254	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323255	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323256	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323257	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323258	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62323259	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325160	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325161	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325189	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62325190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62325192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325193	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325194	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325198	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325200	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325201	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325202	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325204	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325206	1.00[EUR][1000 genomes]
rs62325208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325211	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325212	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325213	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62325239	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62325240	0.81[EUR][1000 genomes]
rs62325241	0.81[EUR][1000 genomes]
rs62325242	0.81[EUR][1000 genomes]
rs62325245	0.83[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	0.81[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: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
rs62325184	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

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	chr4:99934800-99944800	Weak transcription	Small Intestine	intestine
4	chr4:99935000-99945400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:99935400-99945600	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:99935600-99944400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr4:99937600-99944400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:99937600-99966200	Weak transcription	HUVEC	blood vessel
9	chr4:99938200-99944400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:99938800-99944400	ZNF genes & repeats	Fetal Muscle Leg	muscle
11	chr4:99938800-99945600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:99939400-99944400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
13	chr4:99940000-99944000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
14	chr4:99940200-99944000	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr4:99940800-99944000	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
16	chr4:99940800-99944200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
17	chr4:99940800-99944400	ZNF genes & repeats	GM12878-XiMat	blood
18	chr4:99941000-99944200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:99941000-99944400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:99941000-99944400	ZNF genes & repeats	Fetal Thymus	thymus
21	chr4:99941400-99944000	ZNF genes & repeats	Fetal Intestine Large	intestine
22	chr4:99941400-99944200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:99941400-99944400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:99941400-99944400	ZNF genes & repeats	Fetal Stomach	stomach
25	chr4:99941600-99944200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:99941600-99944200	ZNF genes & repeats	Primary B cells from cord blood	blood
27	chr4:99941600-99944400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:99942200-99950400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr4:99942200-99969600	Weak transcription	Fetal Brain Female	brain
30	chr4:99942400-99944000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:99942400-99944200	Strong transcription	Primary T cells from cord blood	blood
32	chr4:99942400-99944200	Enhancers	Right Atrium	heart
33	chr4:99942400-99945600	Weak transcription	Fetal Lung	lung
34	chr4:99942600-99944200	Weak transcription	A549	lung
35	chr4:99942600-99944400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:99942600-99945400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:99942600-99946800	Weak transcription	Psoas Muscle	Psoas
38	chr4:99942600-99950000	Weak transcription	Dnd41	blood
39	chr4:99942600-99953400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:99942800-99944000	Strong transcription	HepG2	liver
41	chr4:99942800-99944200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:99942800-99945000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:99942800-99945400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:99942800-99945600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr4:99942800-99946200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:99942800-99946200	Weak transcription	Ovary	ovary
47	chr4:99942800-99948800	Weak transcription	NHDF-Ad	bronchial
48	chr4:99942800-99955800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:99942800-99957000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:99943000-99944000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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