Variant report

Variant	rs1393565
Chromosome Location	chr9:85605040-85605041
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:85599370..85601315-chr9:85604604..85608125,3	MCF-7	breast:
2	chr9:85604957..85606765-chr9:85610230..85612292,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1008171	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1010480	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs10115768	0.95[EUR][1000 genomes]
rs10116216	0.81[CEU][hapmap]
rs10116254	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs10121156	0.81[EUR][1000 genomes]
rs10121204	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs10121395	1.00[CEU][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes]
rs10126033	0.93[EUR][1000 genomes]
rs10735559	0.89[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs10746694	0.94[EUR][1000 genomes]
rs10780561	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10780562	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10780563	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs10780565	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs10780567	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs10867924	0.84[EUR][1000 genomes]
rs10867925	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10867926	0.81[EUR][1000 genomes]
rs10867928	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10867929	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs1125915	0.81[CEU][hapmap]
rs13302349	0.93[EUR][1000 genomes]
rs1393562	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs1393563	0.89[CEU][hapmap]
rs1393564	0.92[CEU][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes]
rs1502682	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs1502683	0.89[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1502684	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1502685	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1546315	1.00[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1546316	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1546317	1.00[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1580881	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs1976455	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2062761	0.81[CEU][hapmap]
rs2279814	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs29001503	0.89[EUR][1000 genomes]
rs4146960	1.00[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4146961	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4301515	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4348583	0.96[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs4355855	0.89[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs4385545	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4391505	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4460464	0.81[CEU][hapmap]
rs4623517	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4628323	0.88[EUR][1000 genomes]
rs4877244	1.00[CEU][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4877724	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4877725	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6559694	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs6559695	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs7019227	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs7024864	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes]
rs7045914	0.91[EUR][1000 genomes]
rs7847666	1.00[CEU][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7849126	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7853052	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7854101	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs7862012	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7864688	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7866666	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs7867614	0.91[EUR][1000 genomes]
rs952450	1.00[CEU][hapmap];0.91[JPT][hapmap];0.95[EUR][1000 genomes]
rs998119	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv6585	chr9:85566659-85611489	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1393565	WNT10B	trans	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85592800-85608600	Weak transcription	Stomach Mucosa	stomach
2	chr9:85594600-85606000	Weak transcription	Fetal Intestine Large	intestine
3	chr9:85594800-85628200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:85597200-85627000	Weak transcription	A549	lung
5	chr9:85597600-85608600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:85597600-85608600	Weak transcription	HMEC	breast
7	chr9:85603000-85606400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:85603000-85606400	Weak transcription	Fetal Kidney	kidney
9	chr9:85603000-85608600	Weak transcription	Gastric	stomach
10	chr9:85603000-85615800	Weak transcription	Fetal Intestine Small	intestine
11	chr9:85603000-85628200	Weak transcription	Fetal Stomach	stomach
12	chr9:85603200-85621600	Weak transcription	Esophagus	oesophagus
13	chr9:85603200-85643800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:85603400-85612400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:85603600-85607200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:85603800-85605800	Strong transcription	Pancreas	Pancrea
17	chr9:85603800-85613200	Weak transcription	Colonic Mucosa	Colon
18	chr9:85604000-85608600	Weak transcription	Ovary	ovary
19	chr9:85604200-85606400	Weak transcription	Fetal Lung	lung
20	chr9:85604400-85607000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:85605000-85608200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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