Variant report

Variant	rs61220667
Chromosome Location	chr3:52744436-52744437
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT5A	chr3:52744388-52744916	GM12878	blood:	n/a	n/a
2	FOXM1	chr3:52744390-52744886	GM12878	blood:	n/a	n/a
3	IKZF1	chr3:52744398-52744887	GM12878	blood:	n/a	n/a
4	NFIC	chr3:52744416-52745111	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:52743768-52744770	K562	blood:	n/a	n/a
6	RUNX3	chr3:52744362-52744861	GM12878	blood:	n/a	n/a
7	MTA3	chr3:52744249-52744920	GM12878	blood:	n/a	n/a
8	NFIC	chr3:52744274-52745015	GM12878	blood:	n/a	n/a
9	PML	chr3:52744345-52744908	GM12878	blood:	n/a	n/a
10	RUNX3	chr3:52744305-52744984	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52738473..52741784-chr3:52742214..52745484,3	MCF-7	breast:
2	chr3:52738807..52741797-chr3:52744029..52746270,3	K562	blood:
3	chr3:52743756..52745497-chr3:52746997..52749593,2	MCF-7	breast:
4	chr3:52744150..52746226-chr3:52767313..52769534,2	K562	blood:
5	chr3:52743407..52745349-chr3:52750023..52752984,2	K562	blood:

No data

Variant related genes	Relation type
GLT8D1	TF binding region
ENSG00000114902	Chromatin interaction
ENSG00000270941	Chromatin interaction
ENSG00000016864	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10510759	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11510435	1.00[EUR][1000 genomes]
rs12107484	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052357	1.00[EUR][1000 genomes]
rs17052404	1.00[EUR][1000 genomes]
rs1987234	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34173244	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35911561	0.86[AFR][1000 genomes]
rs35920544	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4532127	1.00[EUR][1000 genomes]
rs56134416	1.00[EUR][1000 genomes]
rs56156188	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56259931	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56276589	1.00[EUR][1000 genomes]
rs56665533	1.00[EUR][1000 genomes]
rs57008939	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57246324	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57298447	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57319306	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57560655	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57757646	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57946083	1.00[EUR][1000 genomes]
rs58100002	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	1.00[EUR][1000 genomes]
rs58564212	1.00[EUR][1000 genomes]
rs58725214	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59638016	1.00[EUR][1000 genomes]
rs59869286	1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60415551	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60611300	0.83[AFR][1000 genomes]
rs60682984	0.83[AFR][1000 genomes]
rs60770874	1.00[EUR][1000 genomes]
rs60823713	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs60916588	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61538294	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6445536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762788	1.00[EUR][1000 genomes]
rs6769720	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6780005	0.87[EUR][1000 genomes]
rs6780397	1.00[EUR][1000 genomes]
rs72947580	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72947589	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72950424	1.00[EUR][1000 genomes]
rs72950430	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72950432	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950437	1.00[EUR][1000 genomes]
rs72960212	1.00[EUR][1000 genomes]
rs72960237	1.00[EUR][1000 genomes]
rs72960240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960260	1.00[EUR][1000 genomes]
rs72960274	1.00[EUR][1000 genomes]
rs72960281	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72965181	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	1.00[EUR][1000 genomes]
rs7619643	1.00[AMR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	1.00[EUR][1000 genomes]
rs7647992	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7648016	0.85[AMR][1000 genomes]
rs934839	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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741000-52746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:52741000-52748200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:52741000-52748200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:52741000-52748800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:52741000-52748800	Weak transcription	Lung	lung
6	chr3:52741200-52748200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:52741400-52746600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:52741400-52747000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:52741400-52765600	Weak transcription	Aorta	Aorta
10	chr3:52741400-52766600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:52741600-52746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:52741600-52746400	Weak transcription	Gastric	stomach
13	chr3:52741600-52746400	Weak transcription	Spleen	Spleen
14	chr3:52741600-52746600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:52741600-52747000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:52741600-52747000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:52741600-52748000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:52741600-52748200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:52741600-52748200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:52741600-52748400	Weak transcription	Colonic Mucosa	Colon
21	chr3:52741600-52748400	Weak transcription	Right Ventricle	heart
22	chr3:52741600-52748600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:52741600-52748600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:52741600-52752600	Weak transcription	Ovary	ovary
25	chr3:52741600-52752600	Weak transcription	A549	lung
26	chr3:52741600-52764000	Weak transcription	Small Intestine	intestine
27	chr3:52741600-52765600	Weak transcription	Esophagus	oesophagus
28	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
29	chr3:52741800-52744600	Strong transcription	Fetal Intestine Large	intestine
30	chr3:52741800-52746800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr3:52741800-52747400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:52741800-52748400	Weak transcription	Fetal Heart	heart
33	chr3:52742000-52744600	Genic enhancers	Primary B cells from cord blood	blood
34	chr3:52742000-52744800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:52742000-52744800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:52742000-52744800	Strong transcription	Fetal Intestine Small	intestine
37	chr3:52742000-52744800	Strong transcription	Fetal Stomach	stomach
38	chr3:52742000-52746400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:52742000-52748600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:52742000-52754200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:52742000-52765600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:52742000-52766400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:52742000-52766400	Weak transcription	NHLF	lung
44	chr3:52742000-52766600	Weak transcription	Hela-S3	cervix
45	chr3:52742000-52766600	Weak transcription	NHEK	skin
46	chr3:52742200-52744600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:52742200-52748600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:52742200-52748800	Weak transcription	Stomach Mucosa	stomach
49	chr3:52742200-52767200	Weak transcription	Fetal Brain Male	brain
50	chr3:52742200-52768800	Weak transcription	Colon Smooth Muscle	Colon

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