Variant report

Variant	rs17862847
Chromosome Location	chr2:234549011-234549012
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	2:234543708-234558325..2:234772667-234780240	Hela-S3	cervix:
2	chr2:234544581..234547100-chr2:234548174..234549799,2	MCF-7	breast:
3	2:234543708-234558325..2:234649753-234657866	Hela-S3	cervix:
4	2:234492023-234494396..2:234543708-234558325	GM12878	blood:

Variant related genes	Relation type
ENSG00000224287	Chromatin interaction
ENSG00000227802	Chromatin interaction
ENSG00000228949	Chromatin interaction
ENSG00000242515	Chromatin interaction
ENSG00000228445	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1042605	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929251	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]
rs10929252	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]
rs1113193	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs12479240	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17854828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17862836	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17862837	0.87[ASN][1000 genomes]
rs17862857	0.82[ASW][hapmap];0.91[YRI][hapmap]
rs17863754	0.87[ASN][1000 genomes]
rs17863766	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17863773	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17864684	0.94[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs17868303	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17874938	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1823803	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1901813	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2248733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28967013	0.87[ASN][1000 genomes]
rs28969987	0.88[ASN][1000 genomes]
rs4114768	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4663871	0.91[YRI][hapmap]
rs6706988	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6707134	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6713902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6728792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6731242	0.94[CEU][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7608713	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv3445986	chr2:234494952-234557707	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	esv3419326	chr2:234498411-234560470	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
6	esv2762307	chr2:234504523-234561979	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
7	nsv1007561	chr2:234507291-234560670	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv536181	chr2:234507291-234560670	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv3406377	chr2:234517448-234558127	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv876015	chr2:234518011-234579915	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv961572	chr2:234526394-234559587	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	nsv584704	chr2:234526680-234569137	Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
13	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17862847	ALPI	cis	parietal	SCAN
rs17862847	USP40	Cis_1M	lymphoblastoid	RTeQTL
rs17862847	USP40	cis	cerebellum	SCAN
rs17862847	SPP2	cis	parietal	SCAN
rs17862847	FBXO36	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234547800-234554000	Weak transcription	Colonic Mucosa	Colon
2	chr2:234548200-234549400	Weak transcription	Rectal Mucosa Donor 31	rectum

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