Variant report

Variant	rs939577
Chromosome Location	chr3:112022205-112022206
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr3:112021224-112022933	H1-hESC	embryonic stem cell:	n/a	n/a
2	ATF2	chr3:112021890-112022672	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:112021832-112022401	H1-hESC	embryonic stem cell:	n/a	n/a
4	TBP	chr3:112021868-112022946	H1-hESC	embryonic stem cell:	n/a	n/a
5	POU5F1	chr3:112021866-112022496	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:112021831-112022258	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:112020833-112022650	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr3:112021899-112022338	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:112022131-112022228	HUVEC	blood vessel:	n/a	n/a
10	SIN3A	chr3:112021596-112022928	H1-hESC	embryonic stem cell:	n/a	n/a
11	HDAC2	chr3:112021936-112022310	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTBP2	chr3:112021346-112022312	H1-hESC	embryonic stem cell:	n/a	n/a
13	MTA3	chr3:112022028-112022895	GM12878	blood:	n/a	n/a
14	RAD21	chr3:112021910-112022709	H1-hESC	embryonic stem cell:	n/a	n/a
15	RAD21	chr3:112021872-112022331	H1-hESC	embryonic stem cell:	n/a	n/a
16	ATF2	chr3:112021897-112022624	H1-hESC	embryonic stem cell:	n/a	n/a
17	CEBPB	chr3:112021901-112022660	H1-hESC	embryonic stem cell:	n/a	n/a
18	YY1	chr3:112021925-112022487	H1-hESC	embryonic stem cell:	n/a	n/a
19	SP1	chr3:112021863-112023047	H1-hESC	embryonic stem cell:	n/a	chr3:112022141-112022152
20	SP1	chr3:112021821-112022488	H1-hESC	embryonic stem cell:	n/a	chr3:112022141-112022152
21	TEAD4	chr3:112021937-112022442	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:112022135-112023055	GM12892	blood:	n/a	n/a
23	EP300	chr3:112021919-112022329	H1-hESC	embryonic stem cell:	n/a	n/a
24	NANOG	chr3:112022122-112022292	H1-hESC	embryonic stem cell:	n/a	n/a
25	BACH1	chr3:112022005-112022406	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr3:112021951-112022439	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAF1	chr3:112021840-112022466	H1-hESC	embryonic stem cell:	n/a	n/a
28	TEAD4	chr3:112021873-112022512	H1-hESC	embryonic stem cell:	n/a	n/a
29	CHD2	chr3:112021818-112022916	H1-hESC	embryonic stem cell:	n/a	n/a
30	CHD1	chr3:112021904-112022583	H1-hESC	embryonic stem cell:	n/a	n/a
31	EGR1	chr3:112021940-112022369	H1-hESC	embryonic stem cell:	n/a	n/a
32	GTF2F1	chr3:112021927-112022643	H1-hESC	embryonic stem cell:	n/a	n/a
33	ZNF143	chr3:112021133-112023008	H1-hESC	embryonic stem cell:	n/a	n/a
34	TAF1	chr3:112021808-112022350	H1-hESC	embryonic stem cell:	n/a	n/a
35	EGR1	chr3:112021849-112022430	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr3:112021905-112022537	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF7	chr3:112021843-112022422	H1-hESC	embryonic stem cell:	n/a	n/a
38	MYC	chr3:112022053-112022548	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:112021187-112022691	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000239482	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11714917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716857	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073116	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17513726	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2280462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2399411	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4550804	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56037521	0.83[ASN][1000 genomes]
rs62264134	0.83[ASN][1000 genomes]
rs62264135	0.83[ASN][1000 genomes]
rs62264136	0.83[ASN][1000 genomes]
rs62264137	0.83[ASN][1000 genomes]
rs6438066	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438067	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs6771014	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774405	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6809034	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7619941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs939576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814088	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818526	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv3949	chr3:111998512-112044060	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv967052	chr3:112020436-112027937	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112016600-112022400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:112021000-112022400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:112021000-112022400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
4	chr3:112021000-112023000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:112021200-112022400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:112021200-112023400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr3:112021400-112022600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:112021400-112023000	Active TSS	Brain Cingulate Gyrus	brain
9	chr3:112021400-112023200	Active TSS	Colon Smooth Muscle	Colon
10	chr3:112021400-112023200	Flanking Active TSS	Fetal Thymus	thymus
11	chr3:112021400-112023400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr3:112021400-112025200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:112021600-112022400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:112021600-112023000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:112021600-112023000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:112021600-112023000	Active TSS	Right Atrium	heart
17	chr3:112021600-112023200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:112021600-112023400	Active TSS	Fetal Brain Female	brain
19	chr3:112021600-112023400	Active TSS	Rectal Smooth Muscle	rectum
20	chr3:112021600-112023600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:112021800-112022400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:112021800-112022400	Enhancers	Primary T cells fromperipheralblood	blood
23	chr3:112021800-112022400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr3:112021800-112022400	Weak transcription	Esophagus	oesophagus
25	chr3:112021800-112022400	Flanking Active TSS	Fetal Heart	heart
26	chr3:112021800-112022400	Flanking Active TSS	NH-A	brain
27	chr3:112021800-112022600	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr3:112021800-112022600	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr3:112021800-112022600	Flanking Active TSS	NHLF	lung
30	chr3:112021800-112022800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:112021800-112022800	Active TSS	Hela-S3	cervix
32	chr3:112021800-112023000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:112021800-112023000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:112021800-112023000	Active TSS	Aorta	Aorta
35	chr3:112021800-112023000	Active TSS	Placenta	Placenta
36	chr3:112021800-112023200	Active TSS	Colonic Mucosa	Colon
37	chr3:112021800-112023400	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr3:112021800-112023400	Active TSS	Left Ventricle	heart
39	chr3:112021800-112023400	Flanking Active TSS	HUVEC	blood vessel
40	chr3:112021800-112023600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:112021800-112023600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr3:112021800-112023600	Enhancers	Lung	lung
43	chr3:112021800-112023600	Active TSS	Psoas Muscle	Psoas
44	chr3:112022000-112022400	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr3:112022000-112022400	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr3:112022000-112022400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:112022000-112022400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:112022000-112022400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr3:112022000-112022400	Flanking Active TSS	Thymus	Thymus
50	chr3:112022000-112022400	Flanking Active TSS	GM12878-XiMat	blood

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