Variant report

Variant	rs6559694
Chromosome Location	chr9:85613043-85613044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1008171	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1010480	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10115768	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10116216	0.81[CEU][hapmap];0.88[MEX][hapmap]
rs10116254	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10121156	0.80[EUR][1000 genomes]
rs10121204	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10121376	0.84[EUR][1000 genomes]
rs10121395	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10126033	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10735559	0.89[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs10746694	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10780561	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs10780562	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10780563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780564	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10780565	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10780567	1.00[CEU][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10867924	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10867925	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10867926	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10867927	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10867928	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10867929	1.00[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10867930	0.85[JPT][hapmap]
rs1125915	0.81[CEU][hapmap]
rs13302349	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1393562	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1393563	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1393564	0.92[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1393565	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1502682	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1502683	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs1502684	0.89[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs1502685	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1546315	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1546316	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1546317	1.00[CEU][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1580881	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1976455	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1995423	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs2062761	0.81[CEU][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs2279814	1.00[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs29001503	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4146960	1.00[CEU][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4146961	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4301515	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4348583	0.96[CEU][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4355855	0.89[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs4385545	1.00[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4391505	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs4460464	0.81[CEU][hapmap];0.88[MEX][hapmap]
rs4623517	1.00[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4628323	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4877244	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4877725	0.89[CEU][hapmap]
rs4877726	0.90[JPT][hapmap]
rs6559693	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559695	0.96[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7019227	1.00[CEU][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7024864	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7029133	0.85[AMR][1000 genomes]
rs7045914	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7847666	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7854101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864688	0.83[EUR][1000 genomes]
rs7866666	1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7867614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872982	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs871512	0.90[JPT][hapmap];0.80[MEX][hapmap]
rs952450	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs998119	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050771	chr9:85416931-85643417	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6559694	AGTPBP1	cis	parietal	SCAN
rs6559694	WNT10B	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85594800-85628200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:85597200-85627000	Weak transcription	A549	lung
3	chr9:85603000-85615800	Weak transcription	Fetal Intestine Small	intestine
4	chr9:85603000-85628200	Weak transcription	Fetal Stomach	stomach
5	chr9:85603200-85621600	Weak transcription	Esophagus	oesophagus
6	chr9:85603200-85643800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr9:85603800-85613200	Weak transcription	Colonic Mucosa	Colon
8	chr9:85608800-85628000	Weak transcription	Fetal Kidney	kidney
9	chr9:85609200-85616200	Strong transcription	Pancreas	Pancrea
10	chr9:85609400-85616600	Weak transcription	Stomach Mucosa	stomach
11	chr9:85609400-85620800	Weak transcription	Gastric	stomach
12	chr9:85610800-85642000	Weak transcription	Fetal Intestine Large	intestine
13	chr9:85611800-85613400	Enhancers	HMEC	breast
14	chr9:85611800-85614000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:85611800-85615600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr9:85612000-85617000	Weak transcription	Fetal Lung	lung
17	chr9:85612200-85613400	Weak transcription	Fetal Brain Male	brain
18	chr9:85612400-85616200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr9:85612800-85616800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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