Variant report

Variant	rs7623762
Chromosome Location	chr3:142428926-142428927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142428790..142430856-chr3:142431649..142434549,3	K562	blood:
2	chr3:142428329..142432117-chr3:142439414..142444140,4	K562	blood:
3	chr3:142427916..142430290-chr3:142431838..142434549,2	K562	blood:

Variant related genes	Relation type
ENSG00000144935	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11715459	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11915805	0.85[AMR][1000 genomes]
rs1382688	0.82[ASW][hapmap]
rs1604	0.89[AMR][1000 genomes]
rs2049328	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2177398	0.82[ASW][hapmap]
rs2354856	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs28571594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35467195	0.86[AMR][1000 genomes]
rs35862982	0.86[AMR][1000 genomes]
rs3773504	0.83[MKK][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3821647	0.88[CHB][hapmap]
rs4259003	0.88[CHB][hapmap]
rs4539980	0.86[AMR][1000 genomes]
rs55722917	0.89[AMR][1000 genomes]
rs56775607	0.86[AMR][1000 genomes]
rs6440104	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440105	0.98[ASN][1000 genomes]
rs6440106	0.86[AMR][1000 genomes]
rs6440107	0.94[ASW][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes]
rs67100994	0.98[ASN][1000 genomes]
rs6784998	0.94[ASW][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes]
rs6790959	0.89[AMR][1000 genomes]
rs7621642	0.82[ASW][hapmap]
rs7626908	0.86[AMR][1000 genomes]
rs7628728	0.89[YRI][hapmap];0.89[AMR][1000 genomes]
rs7629129	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7631245	0.82[CHB][hapmap]
rs7637846	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs7638459	0.82[ASW][hapmap]
rs7639403	0.82[ASW][hapmap]
rs7641514	0.88[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap]
rs7644704	0.89[AMR][1000 genomes]
rs7647291	0.88[YRI][hapmap];0.89[AMR][1000 genomes]
rs953239	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes]
rs953641	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9815607	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs9820721	0.87[AMR][1000 genomes]
rs9823836	0.81[AMR][1000 genomes]
rs9849265	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9861598	0.83[AMR][1000 genomes]
rs9865053	0.84[AMR][1000 genomes]
rs9868886	0.82[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591920	chr3:142411200-142496951	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv521098	chr3:142411200-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv520533	chr3:142417070-142440299	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv518623	chr3:142417070-142503605	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7623762	CHST2	cis	lymphoblastoid	seeQTL
rs7623762	PLS1	cis	cerebellum	SCAN
rs7623762	ATP1B3	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142366000-142435400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142389800-142442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:142392800-142433000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:142408800-142430400	Weak transcription	Liver	Liver
5	chr3:142424600-142430200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:142425800-142431000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:142426200-142435000	Weak transcription	Fetal Intestine Large	intestine
8	chr3:142427000-142430600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:142427000-142430600	Weak transcription	Rectal Mucosa Donor 31	rectum

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