Variant report

Variant	rs3757995
Chromosome Location	chr8:95202103-95202104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:94751681..94753437-chr8:95200264..95202250,2	MCF-7	breast:
2	chr8:95200401..95202545-chr8:95205826..95207380,2	K562	blood:
3	chr8:95201827..95203670-chr8:95208153..95211021,2	MCF-7	breast:
4	chr8:95200777..95202734-chr8:95202948..95204607,2	K562	blood:

Variant related genes	Relation type
ENSG00000183808	Chromatin interaction
ENSG00000253848	Chromatin interaction
ENSG00000212998	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10504934	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10956904	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10956905	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10956906	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11777372	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11779791	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11786049	0.82[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12056835	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12114629	0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs1350283	0.85[CEU][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17727794	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1817245	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1971965	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2613221	1.00[ASN][1000 genomes]
rs2623177	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs34689002	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3886489	0.93[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4587298	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4734271	0.84[EUR][1000 genomes]
rs55795711	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56129387	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59605341	0.94[ASN][1000 genomes]
rs59773910	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60945589	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62523262	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62523265	0.95[ASN][1000 genomes]
rs62523266	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62523277	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62523279	0.81[ASN][1000 genomes]
rs6981215	0.82[ASN][1000 genomes]
rs723360	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs755917	0.81[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.83[ASN][1000 genomes]
rs7819765	0.82[ASN][1000 genomes]
rs874019	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs900051	0.85[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs9642922	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9643341	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs978639	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024907	chr8:95188944-95296378	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv539677	chr8:95188944-95296378	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1022972	chr8:95189085-95245392	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1024893	chr8:95189085-95293557	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv518636	chr8:95196794-95233336	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv539678	chr8:95197036-95225644	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1030292	chr8:95198982-95231692	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv522024	chr8:95199215-95232449	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1020665	chr8:95199302-95232062	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3757995	PGCP	cis	cerebellum	SCAN
rs3757995	LAPTM4B	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95189800-95205800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr8:95196600-95202600	Weak transcription	Small Intestine	intestine
3	chr8:95200000-95202800	Genic enhancers	Duodenum Mucosa	Duodenum
4	chr8:95200000-95210200	Genic enhancers	Fetal Intestine Small	intestine
5	chr8:95200600-95207400	Genic enhancers	Fetal Intestine Large	intestine
6	chr8:95201200-95210800	Weak transcription	Pancreas	Pancrea
7	chr8:95201400-95202400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr8:95201600-95202600	Weak transcription	Colonic Mucosa	Colon
9	chr8:95201600-95203000	Weak transcription	Stomach Mucosa	stomach
10	chr8:95201800-95202200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr8:95202000-95203400	Genic enhancers	Sigmoid Colon	Sigmoid Colon

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