Variant report

Variant	rs2741042
Chromosome Location	chr2:234565917-234565918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234557472..234561426-chr2:234563315..234566249,3	K562	blood:
2	chr2:234564130..234566542-chr2:234601879..234604853,2	MCF-7	breast:
3	chr2:234559926..234563165-chr2:234564749..234566368,3	K562	blood:

Variant related genes	Relation type
ENSG00000167165	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2602362	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs2602374	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602376	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2741012	0.95[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741013	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741022	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741023	1.00[ASN][1000 genomes]
rs2741024	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2741027	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2741030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741034	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2741044	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2741045	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2741046	1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28898569	0.82[YRI][hapmap]
rs28898572	0.82[YRI][hapmap]
rs28898588	0.82[YRI][hapmap]
rs28898597	0.82[YRI][hapmap]
rs28898607	0.82[YRI][hapmap]
rs28898610	0.82[YRI][hapmap]
rs28898618	0.82[YRI][hapmap]
rs28899169	0.82[YRI][hapmap]
rs28899184	0.82[YRI][hapmap]
rs28899185	0.82[YRI][hapmap]
rs28969677	0.82[YRI][hapmap]
rs28969714	0.82[YRI][hapmap]
rs6746419	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2741042	IQCA1	cis	cerebellum	SCAN
rs2741042	NPPC	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234554600-234587800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:234559800-234592800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:234564200-234566800	Weak transcription	Liver	Liver

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