Variant report

Variant	rs17533702
Chromosome Location	chr9:96361228-96361229
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96356589..96359432-chr9:96360730..96362532,3	MCF-7	breast:
2	chr9:96353399..96355498-chr9:96360574..96362233,2	MCF-7	breast:
3	chr9:96360523..96363170-chr9:96791187..96793107,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158079	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1000850	0.82[CHD][hapmap]
rs1000852	0.85[CHD][hapmap]
rs10122092	0.83[CHD][hapmap]
rs10821170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821171	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992794	0.94[ASN][1000 genomes]
rs10992795	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992796	0.89[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13290276	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13296529	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2254712	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2265300	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2265574	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2265575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2265576	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2989753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2989755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2989756	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2994365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2994369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2994370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073155	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743929	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744255	0.87[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.93[ASN][1000 genomes]
rs4744258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744259	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56351334	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62573991	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62574558	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs928368	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9409477	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9644969	0.85[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17533702	FAM120AOS	Cis_1M	lymphoblastoid	RTeQTL
rs17533702	PTCH1	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96341800-96362200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr9:96345000-96362600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr9:96349000-96365800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:96352400-96366000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:96352400-96369200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:96352400-96384600	Weak transcription	NHLF	lung
7	chr9:96352600-96362400	Weak transcription	Fetal Lung	lung
8	chr9:96354200-96361400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:96355000-96361800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:96355200-96362600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:96355200-96362800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:96355200-96362800	Weak transcription	Brain Angular Gyrus	brain
13	chr9:96355400-96361400	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:96356400-96364000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr9:96356600-96365600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:96356800-96362600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:96357000-96361400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:96357000-96361400	Weak transcription	NHDF-Ad	bronchial
19	chr9:96357000-96361600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr9:96357000-96362200	Weak transcription	Small Intestine	intestine
21	chr9:96357000-96362400	Weak transcription	HSMM	muscle
22	chr9:96357000-96362600	Weak transcription	A549	lung
23	chr9:96357000-96367000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:96357200-96361800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:96357200-96361800	Weak transcription	K562	blood
26	chr9:96357200-96362400	Weak transcription	Hela-S3	cervix
27	chr9:96357200-96362800	Weak transcription	HMEC	breast
28	chr9:96357400-96362400	Weak transcription	NHEK	skin
29	chr9:96357600-96364200	Enhancers	Pancreas	Pancrea
30	chr9:96357600-96364600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:96357800-96362600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:96358200-96363000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr9:96358200-96363600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:96358400-96363000	Enhancers	Right Atrium	heart
35	chr9:96358400-96364000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr9:96358400-96365200	Enhancers	Primary B cells from peripheral blood	blood
37	chr9:96359200-96364000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr9:96359400-96362600	Enhancers	Primary T cells from cord blood	blood
39	chr9:96359600-96361600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:96359600-96361600	Enhancers	Spleen	Spleen
41	chr9:96359600-96363000	Enhancers	Ovary	ovary
42	chr9:96359600-96363200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr9:96359600-96363200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr9:96359600-96363600	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr9:96359600-96363800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:96359600-96363800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr9:96359600-96364200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:96359600-96364200	Enhancers	Lung	lung
49	chr9:96359600-96364400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr9:96359600-96364400	Enhancers	Left Ventricle	heart

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