Variant report

Variant	rs10201177
Chromosome Location	chr2:142896549-142896550
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	EP300	chr2:142896432-142897353	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr2:142896284-142898365	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr2:142896490-142896747	SK-N-SH_RA	brain:	n/a	n/a
4	MXI1	chr2:142896353-142898324	SK-N-SH	brain:	n/a	n/a
5	EP300	chr2:142896469-142897297	SK-N-SH_RA	brain:	n/a	n/a
6	RAD21	chr2:142896469-142896770	SK-N-SH_RA	brain:	n/a	n/a
7	RAD21	chr2:142896326-142898874	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:142894381..142895892-chr2:142895976..142898134,2	K562	blood:
2	chr2:142888202..142889034-chr2:142896341..142897145,2	MCF-7	breast:

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

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10164457	0.90[CEU][hapmap]
rs10179879	0.90[CEU][hapmap]
rs10187861	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194564	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10197442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201480	0.81[CEU][hapmap]
rs11888082	0.90[CEU][hapmap]
rs12691633	0.90[CEU][hapmap]
rs12994651	0.90[CEU][hapmap]
rs13012748	0.90[CEU][hapmap]
rs13382235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385180	0.90[CEU][hapmap]
rs13392919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13400121	0.81[CEU][hapmap]
rs13405280	0.90[CEU][hapmap]
rs13417943	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13418304	0.90[CEU][hapmap]
rs13420312	0.90[CEU][hapmap]
rs1349224	0.90[CEU][hapmap]
rs1449491	0.81[CEU][hapmap]
rs1449502	0.90[CEU][hapmap]
rs16847971	0.90[CEU][hapmap]
rs17832157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982384	0.90[CEU][hapmap]
rs28587375	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35829239	0.96[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4662401	1.00[CHB][hapmap]
rs6721602	0.90[CEU][hapmap]
rs6749591	0.90[CEU][hapmap]
rs6756877	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7574284	0.90[CEU][hapmap]
rs9287333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630925	0.90[CEU][hapmap]

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:3 , 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
2	chr2:142892800-142897000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:142892800-142897200	Weak transcription	Brain Anterior Caudate	brain

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