Variant report

Variant	rs10207741
Chromosome Location	chr2:142898257-142898258
allele	A/G
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	CTCF	chr2:142897825-142898354	SK-N-SH	brain:	n/a	chr2:142898102-142898120 chr2:142898097-142898118 chr2:142898067-142898075
2	CTCF	chr2:142897836-142898365	IMR90	lung:	n/a	chr2:142898102-142898120 chr2:142898097-142898118 chr2:142898067-142898075
3	RAD21	chr2:142897832-142898389	HCT-116	colon:	n/a	n/a
4	RAD21	chr2:142897847-142898342	SK-N-SH_RA	brain:	n/a	n/a
5	RAD21	chr2:142897846-142898308	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr2:142897775-142898314	HepG2	liver:	n/a	n/a
7	BRCA1	chr2:142897936-142898258	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr2:142897915-142898278	K562	blood:	n/a	chr2:142898102-142898120 chr2:142898097-142898118 chr2:142898067-142898075
9	RAD21	chr2:142897897-142898359	MCF-7	breast:	n/a	n/a
10	RAD21	chr2:142897888-142898292	HepG2	liver:	n/a	n/a
11	CTCF	chr2:142897900-142898281	HepG2	liver:	n/a	chr2:142898102-142898120 chr2:142898097-142898118 chr2:142898067-142898075
12	RAD21	chr2:142897865-142898299	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr2:142897919-142898262	A549	lung:	n/a	chr2:142898102-142898120 chr2:142898097-142898118 chr2:142898067-142898075
14	EP300	chr2:142896284-142898365	SK-N-SH	brain:	n/a	n/a
15	RAD21	chr2:142897894-142898272	IMR90	lung:	n/a	n/a
16	RAD21	chr2:142897928-142898301	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr2:142897769-142898398	HCT-116	colon:	n/a	chr2:142898102-142898120 chr2:142898097-142898118 chr2:142898067-142898075
18	SMC3	chr2:142897867-142898271	Hela-S3	cervix:	n/a	n/a
19	RAD21	chr2:142897849-142898367	HCT-116	colon:	n/a	n/a
20	MXI1	chr2:142896353-142898324	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr2:142898220-142898370	GM06990	blood:	n/a	n/a
22	RAD21	chr2:142897901-142898332	ECC-1	luminal epithelium:	n/a	n/a
23	RAD21	chr2:142897836-142898276	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr2:142897993-142898264	HCT-116	colon:	n/a	chr2:142898102-142898120 chr2:142898097-142898118 chr2:142898067-142898075
25	RAD21	chr2:142896326-142898874	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr2:142897889-142898305	GM12878	blood:	n/a	chr2:142898102-142898120 chr2:142898097-142898118 chr2:142898067-142898075
27	CTCF	chr2:142897619-142898428	A549	lung:	n/a	chr2:142898102-142898120 chr2:142898097-142898118 chr2:142898067-142898075
28	RAD21	chr2:142897823-142898295	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:142886506..142889089-chr2:142896828..142901902,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244125	TF binding region
ENSG00000168702	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10188131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896128	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328797	0.87[AMR][1000 genomes]
rs13422148	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429243	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430169	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16856855	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59636122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73963457	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73963462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73963463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9653181	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]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv875254	chr2:142833327-142931146	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006247	chr2:142851056-143289465	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv875255	chr2:142894573-142963976	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv875256	chr2:142894573-142994328	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv875257	chr2:142894573-143041082	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142889200-142900800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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