Variant report

Variant	rs2886644
Chromosome Location	chr1:62676284-62676285
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr1:62676211-62677198	U2OS	brain:	n/a	n/a
2	ATF2	chr1:62675363-62677428	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD2	chr1:62675567-62679535	H1-hESC	embryonic stem cell:	n/a	n/a
4	SMC3	chr1:62675660-62676329	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:62675402-62677410	H1-hESC	embryonic stem cell:	n/a	n/a
6	EP300	chr1:62675965-62676421	Hela-S3	cervix:	n/a	n/a
7	ATF2	chr1:62675552-62677433	H1-hESC	embryonic stem cell:	n/a	n/a
8	JUN	chr1:62675904-62676336	Hela-S3	cervix:	n/a	n/a
9	GTF2F1	chr1:62675517-62679496	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:62675505-62676298	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr1:62675762-62676343	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:62671110-62680443	H1-hESC	embryonic stem cell:	n/a	n/a
13	JUND	chr1:62676022-62676290	HepG2	liver:	n/a	chr1:62676134-62676145
14	JUND	chr1:62675900-62676402	Hela-S3	cervix:	n/a	chr1:62676134-62676145
15	FOSL2	chr1:62675950-62676296	A549	lung:	n/a	n/a
16	TAF7	chr1:62675465-62677366	H1-hESC	embryonic stem cell:	n/a	n/a
17	STAT3	chr1:62675960-62676309	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr1:62675942-62676352	Hela-S3	cervix:	n/a	n/a
19	E2F6	chr1:62675410-62676375	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:62672294-62680406	H1-hESC	embryonic stem cell:	n/a	n/a
21	USF2	chr1:62675641-62677196	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62675861..62676588-chr1:62872539..62873330,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000200174	TF binding region
ENSG00000237227	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12725684	0.82[EUR][1000 genomes]
rs12727452	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728092	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12733177	0.85[EUR][1000 genomes]
rs12738720	0.80[EUR][1000 genomes]
rs12740634	0.82[EUR][1000 genomes]
rs12742559	0.80[EUR][1000 genomes]
rs12743112	0.80[EUR][1000 genomes]
rs12745952	0.86[EUR][1000 genomes]
rs12747871	0.81[EUR][1000 genomes]
rs12753338	0.86[EUR][1000 genomes]
rs12755711	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760006	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123071	1.00[CHB][hapmap]
rs34637535	0.80[EUR][1000 genomes]
rs4625314	0.84[JPT][hapmap]
rs7518470	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv870842	chr1:62644118-62679202	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62664800-62677800	Weak transcription	Placenta	Placenta
2	chr1:62666000-62695400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:62668400-62677200	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr1:62670400-62677200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:62671800-62678200	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr1:62672200-62677400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr1:62673200-62676400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:62673800-62677200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
9	chr1:62673800-62677200	ZNF genes & repeats	Fetal Lung	lung
10	chr1:62674000-62677200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:62674400-62676800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
12	chr1:62674400-62678800	Weak transcription	Colonic Mucosa	Colon
13	chr1:62675000-62676400	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:62675400-62676400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:62675400-62676400	Enhancers	HSMM	muscle
16	chr1:62675400-62676800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:62675400-62677000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
18	chr1:62675400-62677000	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr1:62675600-62676400	ZNF genes & repeats	Fetal Muscle Leg	muscle
20	chr1:62675600-62676400	Enhancers	Hela-S3	cervix
21	chr1:62675600-62676400	Enhancers	HSMMtube	muscle
22	chr1:62675600-62677200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr1:62675800-62677000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:62675800-62677400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:62675800-62684600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:62676000-62676400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:62676000-62676600	ZNF genes & repeats	NHEK	skin
28	chr1:62676200-62676400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:62676200-62676600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
30	chr1:62676200-62676600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:62676200-62680400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:62676200-62683400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:62676200-62683600	Weak transcription	Right Atrium	heart
34	chr1:62676200-62689600	Weak transcription	Placenta Amnion	Placenta Amnion

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