Variant report

Variant	rs1976455
Chromosome Location	chr9:85630621-85630622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:85629458..85632047-chr9:85635209..85636711,2	MCF-7	breast:
2	chr9:85630260..85633245-chr9:85676968..85678631,2	MCF-7	breast:
3	chr9:85629111..85631055-chr9:85634729..85636879,2	MCF-7	breast:
4	chr9:85626061..85627670-chr9:85628324..85631017,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165105	Chromatin interaction

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]
rs1010480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10115768	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10116216	0.81[CEU][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs10116254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121156	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10121204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121376	0.82[EUR][1000 genomes]
rs10121395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10126033	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10735559	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs10746694	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780561	0.91[CEU][hapmap]
rs10780562	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10780563	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10780564	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10780565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10780567	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10867924	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10867925	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10867926	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10867927	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10867928	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10867929	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11139896	0.89[ASN][1000 genomes]
rs1125915	0.81[CEU][hapmap]
rs13302349	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1393562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1393563	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs1393564	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1393565	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]
rs1502682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1502683	0.89[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1502684	0.89[CEU][hapmap]
rs1502685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546315	1.00[CEU][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1546316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1580881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1995423	0.80[MEX][hapmap]
rs2062761	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs2279814	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs29001503	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4146960	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146961	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4301515	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4348583	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4355855	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs4385545	1.00[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs4391505	0.89[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4460464	0.81[CEU][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs4623517	1.00[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs4628323	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4877244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4877724	0.81[EUR][1000 genomes]
rs4877725	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs6559694	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6559695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7019227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7024864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029133	0.91[AMR][1000 genomes]
rs7045914	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7847666	1.00[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7849126	0.80[EUR][1000 genomes]
rs7853052	0.82[EUR][1000 genomes]
rs7854101	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7862012	0.82[EUR][1000 genomes]
rs7866666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7867614	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs871512	0.80[MEX][hapmap]
rs952450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs998119	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][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
rs1976455	WNT10B	trans	cerebellum	SCAN
rs1976455	AGTPBP1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85603200-85643800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr9:85610800-85642000	Weak transcription	Fetal Intestine Large	intestine
3	chr9:85613600-85643400	Weak transcription	Colonic Mucosa	Colon
4	chr9:85617200-85645800	Weak transcription	Stomach Mucosa	stomach
5	chr9:85621000-85645400	Weak transcription	Gastric	stomach
6	chr9:85623600-85634800	Weak transcription	Pancreas	Pancrea
7	chr9:85623600-85643200	Weak transcription	Fetal Intestine Small	intestine
8	chr9:85628400-85634800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:85628600-85632000	Weak transcription	Fetal Kidney	kidney
10	chr9:85628600-85643400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:85629000-85636000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr9:85629000-85638800	Weak transcription	Fetal Stomach	stomach
13	chr9:85630000-85641600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:85630600-85633000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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